Analyst® 1.6.2 Release Notes
Analyst® 1.6.2 Software
Release Notes
RUO-IDV-03-0236-A
Release Date: July 2013
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Contents
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
How to Use These Release Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Chapter 2 Enhancements and Fixes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
New Enhancements and Fixes in Analyst 1.6.2 Software . . . . . . . . . . . . . . . . . . .9
New Features and Enhancements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Fixed Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
New Enhancements and Fixes in Analyst 1.6.1 Software . . . . . . . . . . . . . . . . . .13
New Features and Enhancements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Fixed Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
New Enhancements and Fixes in Analyst 1.6 Software Components for
6500 Series Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
New System Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Fixed Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Known Issues and Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
New Enhancements and Fixes in Analyst 1.6 Software . . . . . . . . . . . . . . . . . . .21
New Enhancements and Fixes in the Analyst 1.5.2 Software with HotFixes
to February 2011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
AAO and Companion Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
Acquire — Acquisition and Batch Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26
Configure — Hardware Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26
Explore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Explore — Library Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Firmware Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28
Help Files and Tutorials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28
Quantitate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28
Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29
Program Shortcuts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29
Device Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30
New Enhancements and Fixes in the Analyst 1.5.1 HotFix . . . . . . . . . . . . . . . .30
Acquire . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30
Quantitate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30
Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Fixed Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Acquire . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .32
Quantitate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .32
New Enhancements and Fixes for the Analyst 1.5.1 Software . . . . . . . . . . . . . .32
Configure — Hardware Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .34
Acquire — Acquisition and Batch Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . .34
Tune and Configure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Quantitate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Compatible Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Audit Trail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
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Acquire — Acquisition and Batch Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
Acquire — Information Dependent Acquisition (IDA) and
IDA Method Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38
Quantitate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
Other . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
New Enhancements and Fixes in the Analyst 1.5
Components for 5500 Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Acquire — Acquisition and Batch Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Other . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Notes on Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
New Enhancements and Fixes in the Analyst 1.5
Software and the Analyst 1.4.2 HotFixes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
Audit Trail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
Acquire — Acquisition and Batch Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Tune and Calibrate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Explore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Quantitate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Peripheral Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Other . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Chapter 3 Notes on Use, Known Issues, and Limitations . . . . . . . . . . . . . . . . . 53
Guidance for Antivirus and Backup Software . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Guidance on File Encryption . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Audit Trail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Configure — Administration/Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Configure — Hardware Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .56
Configure — Acquisition Method Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57
Tune and Calibrate — Compound Optimization . . . . . . . . . . . . . . . . . . . . . . . . .58
Tune and Calibrate — Instrument Optimization . . . . . . . . . . . . . . . . . . . . . . . . .58
Tune and Calibrate — Manual Tuning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .60
Acquire — IDA and IDA Method Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .62
Acquire — Method / Batch Editor/Queue Manager . . . . . . . . . . . . . . . . . . . . . . .64
Acquire — Scheduled MRM Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Acquire — Network Data Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70
Explore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .72
Explore — Library Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
Explore — WIFF Data File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76
Quantitate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76
Analyst Software Reporter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
Installer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
Other . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
Compatible Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83
Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .84
Peripheral Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86
CTC PAL / Leap Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86
Shimadzu Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .88
LC Packings Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
DAD Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Agilent Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Tempo MDLC System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .94
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Chapter 4 21 CFR Part 11 Compliance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Appendix A Programs and Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .97
Appendix B Technical Information Regarding Integration . . . . . . . . . . . . . . . . .99
Integration Issue Addressed in the Analyst® 1.4.2 Software . . . . . . . . . . . . . . .99
Changes Introduced in the Analyst 1.5 Software . . . . . . . . . . . . . . . . . . . . . . . .99
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1
Introduction
Thank you for choosing AB SCIEX to supply your LC/MS/MS system. We are pleased to give you
the Analyst® 1.6.2 software, the most comprehensive LC/MS/MS software package available.
The Analyst® 1.6.2 Software Release Notes describe the many new features introduced in the
Analyst 1.6.2 software, as well as workarounds for possible issues. Use these release notes for
reference as you become familiar with the software, and for future reference. For installation and
software compatibility information, see the Analyst® 1.6.2 Software Installation Guide.
Support
At AB SCIEX, we are committed to providing the highest level of support for our Analyst software
users. To obtain answers to questions about any of our products, report problems, or suggest
improvements, visit www.absciex.com. For on-site service, support, and training, visit
www.absciex.com/FAQ or www.absciex.com/training.
How to Use These Release Notes
To help you understand what is new and what is fixed relative to your current Analyst software
version, the Analyst 1.6.2 software release notes have been structured so that you only have to
read the sections that are relevant to you.
Note: For reference, the name of the software patch or HotFixes release where the
issue was previously fixed is included.
Read New Enhancements and Fixes in Analyst 1.6.2 Software on page 9 of the release notes
and then also read up to and including the section describing the software version you are
upgrading from.
Everyone should read Notes on Use, Known Issues, and Limitations on page 53, as this section
applies specifically to issues that are known in the Analyst 1.6.2 software.
Note: The numbers in brackets are reference numbers to each issue or feature in our
internal tracking system.
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2
Enhancements and Fixes
New Enhancements and Fixes in Analyst 1.6.2
Software
New Features and Enhancements
Added support for Windows 7 (64-bit) operating system (OS)
The Analyst® 1.6.2 software now supports Windows 7 (64-bit) SP1 OS and it continues to
support Windows 7 (32-bit) SP1 and Windows XP SP3 operating systems.
Added support for all mass spectrometers
The Analyst 1.6.2 software supports all current triple quadrupole and QTRAP® instruments
including support for SelexION™ technology on the 5500 and 6500 series of instruments.
New Scheduled MRM™ Pro Algorithm
The Scheduled MRM Pro algorithm offers enhancements that improve flexibility and data quality
for users who monitor large numbers of transitions per experiment.
Added support for MS Office 2013 for the Reporter 3.2 Software
The Reporter 3.2 software included with the Analyst 1.6.2 software can now print reports using
MS Office 2007, 2010, or 2013.
New cable-free synchronization mode for autosamplers using AAO
A new synchronization mode has been added to the Method Editor to allow autosampler
synchronization without the use of the AUX I/O cable. This is only applicable to AAO-controlled
devices with drivers supporting this synchronization mode.
New firmware for 4500, 5500, and 6500 series instruments
The firmware for the 4500, 5500, and 6500 series of instruments has been harmonized into a
single version. It also supports SelexION technology on the 5500 and 6500 series instruments.
There are no changes that affect data or data quality. For information on how to upgrade the
firmware of your mass spectrometer, refer to the Installation Guide for the Analyst 1.6.2 software.
Change to inter-scan operation for MRM Scheduled™ MRM Algorithm scans
A change has been made to inter-scan timings for the 4500 and 6500 series of instruments. The
changes provide improved signal stability and reduce crosstalk in all scans included those using
SelexION™ technology. In some cases signal intensity might increase slightly. (AN-238)
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Enhancements and Fixes
Target Scan Time was incorrectly applied for methods with two Scheduled MRM
Algorithm experiments
When a method was created with two Scheduled MRM™ algorithm experiments, if the user
specified differing target scan times for each Scheduled MRM algorithm experiment, the software
would apply the scan time of the second experiment for both. This has been corrected, and each
experiment will use the target scan time assigned in the method. (AN-155)
Cycle time calculation changed for methods with two Scheduled MRM Algorithm
experiments
When creating a method with two Scheduled MRM algorithm experiments, the Analyst software
now optimizes the cycle time which might result in dwell times being calculated lower than in
previous releases. As a result, users running a method that was also run previous to the Analyst
1.6.2 software might now notice more data points being collected in the same period of time.
(AN-155)
Documentation Changes
The Analyst 1.6.2 software does not include Ion Source Guides and Site Planning Guides. Ion
source guides are now delivered with the ion sources, and the Site Planning Guides are available
on the AB SCIEX Web site, http://www.absciex.com/downloads/mass-spectrometry-user-guides.
Retention time up to two decimal places is now displayed in saved Scheduled
MRM Algorithm methods opened in the Analyst 1.6.2 software
The Analyst 1.6.2 software allows the user to enter a value with two decimal places in the Time
(min) column. This value is used for acquisition and is displayed in File Info. When the saved
Scheduled MRM algorithm method was opened in the Acquisition Method Editor, retention time
values entered with two decimal places were only displayed up to one decimal place in the Time
(min) column. This issue has been corrected and now retention time up to two decimal places is
displayed. (AN-221)
Fixed Issues
Data files were being saved in the wrong data file during network acquisition
In very rare cases, when acquiring to network locations it was possible for data to be stored in the
wrong data file. This has been corrected. (AN-25)
Certain character combinations could cause acquisition issues
When acquiring data, the Analyst software was unable to acquire properly if the data folder had
certain character combinations in the name. This would lead to failed acquisitions. The issue has
been corrected. (AN-24)
Reporter — Users could create and print report for the Results Table that was
changed but not saved
Previously, users could print Results Tables that contained unsaved changes, using the Reporter
software. The behavior of the Analyst software has been changed and now the software displays
a message prompting the user to save the changes in the Results Table before printing the
report. (AN-231)
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Enhancements and Fixes
Analyst® 1.6 Patch for Agilent G4234 Column Selection Valve
The Analyst® 1.6 Patch for Agilent G4234 Column Selection Valve adds support for the G4234
Column Selection Valve when installed in the Agilent 1290 G1316C Thermostatted Column
Compartment. This patch functionality is included in the Analyst 1.6.2 software. (AN-10)
GS2 parameter remains editable when IonDrive™ Turbo V Ion Source is being
used
Previously, the GS2 parameter was editable when the IonDrive Turbo V Ion Source was used
with the APCI probe on the 6500 series of instruments, but no gas was actually applied. This
issue has been corrected, and the GS2 parameter is greyed out when the IonDrive Turbo V Ion
Source with APCI probe is used on the 6500 series of instruments. (AN-40)
Reports generated using the Reporter software do not display the names of the
4500, 5500, and 6500 series instruments
The reports generated using the Reporter software were not displaying the instrument name for
data acquired with the 4500, 5500, and 6500 series instruments. This issue has been corrected.
(AN-17)
Analyst® 1.6.1 Patch for Empty Password Issue added in Analyst 1.6.2 Software
The Analyst® 1.6.1 Patch for Empty Password Issue fixed an issue in which entering a ‘blank’
password into an e-signature window after entering the correct password would cause the
Analyst service to crash. This patch functionality is included in the Analyst 1.6.2 software.
(AN-30)
Analyst® 1.6.1 Patch for Agilent Devices
The Analyst® 1.6.1 Patch for Agilent Devices added support for acquisition with the Agilent
Series 1260 G1329B (Standard) autosampler. It also provided a fix for hardware profile activation
failure with the Agilent Series 1200 G1315C DAD. The G1315C DAD can now be activated
successfully and used for acquisition. (AN-26)
Log-on User field in File Info displays N/A in Windows 7 OS
When a user submitted a batch and closed the Analyst software before acquisition was
completed, the File Info of samples acquired after the software was closed displayed N/A in the
Log-on User field in File Info. This issue only existed on Windows 7 and has been corrected.
(AN-47)
Calculated Concentration values were not updated if Dilution Factor for Standard
was set to zero in the Results Table
If the Dilution Factor for the Standard was set to zero, the values in the Calculated Concentration
field were not being updated in the Results Table. This issue has been corrected. (AN-51)
Network Acquisition could cause checksum failure
When running a network acquisition with datafile checksums enabled, the checksum of the
acquired network datafile is verified at the end of the batch. As part of this verification, the datafile
must be opened. However, if the local cache file has not been copied to the network yet, the open
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operation will fail and lead to an invalidation of the checksum. This issue has been corrected.
(AN-83)
Report still generated when Cancel was selected in eSignature dialog
When the Reason Prompt and E-Signature check boxes were selected for the Printing document
on printer event in the Audit Map editor, and a report was printed from a Results Table, the report
was still generated even when Cancel was pressed in the eSignature window. This issue has
been fixed. (AN-129)
Checksum validation added in quantitation
During quantitation, when the user selects a sample to add using the Add/Remove samples, the
software verifies whether the checksum is enabled and if the .wiff file has a valid checksum. If the
checksum is invalid, then a message is shown informing the user and the file is not used for
quantitation. (AN-156)
Checksum validation added before running a sample
If the user tries to acquire a sample to a .wiff file with an invalid checksum, then that sample is
aborted, and an error message is shown. The batch continues to the next sample. If all of the
samples in the batch are stored in the same wiff file, then the rest of the batch is aborted, sample
by sample. When the checksum validation fails, an audit trial entry is entered in the project
section of the audit trail. (AN-156)
Checksum validation added in Manual Tune
In Manual Tune, when the user tries to acquire manual tune data to a data file with an invalid
checksum, the checksum validation fails. When the checksum validation fails, an audit trail entry
is entered in the project section of the audit trail. (AN-156)
Checksums may be invalid or not written at all if acquisition to a network location
is aborted
If an acquisition with datafile checksums enabled to a network location is aborted due to an
instrument or device fault, the resulting file might have either an invalid or no checksum
recorded. In general, failed or aborted samples should not be used for data analysis, as the
conditions leading to the failure may result in improper or incomplete data being collected. This
issue has been fixed. (AN-188)
Audit Trail archive can be lost during archival process over the Network
When the audit trail file (project.atd) reaches 1000 records, it will be archived. If the root project is
located on a network drive, the audit trail archive can be lost if connectivity to the network is lost
during the archiving process. This issue has been corrected. (AN-184)
File Information shows incorrect units/values for Total Scan Time field in a
Scheduled MRM Algorithm method
The File Information of a .wiff file generated using a Scheduled MRM algorithm method displayed
the value and unit of the Target Scan Time field incorrectly as 1000 sec instead of 1000 msec or
1 sec. This issue has been corrected. (AN-190)
Analyst® 1.6.2 Software
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Release Notes
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Enhancements and Fixes
The MRM3 Optimization script is not supported on Windows 7
For Windows 7 users, using the MRM3 Optimization script causes the AnalystService to stop
responding. This script is not supported for Windows 7. This issue has been corrected. (ST
33878)
New Enhancements and Fixes in Analyst 1.6.1
Software
New Features and Enhancements
4500 Series Instrument support
The Analyst 1.6.1 software adds support for the following new instruments:
•
AB SCIEX QTRAP® 4500 system
•
AB SCIEX Triple Quad™ 4500 system
Shimadzu SIL-30ACMP and CTO-30AS
The Analyst 1.6.1 software adds support for the Shimadzu SIL-30ACMP autosampler and CTO30AS column oven.
Method Converter for the 4500 Series of Instruments
The Method Converter script has been updated to allow conversion of existing methods to be
used on the 4500 Series of instruments. In addition, several enhancements and improvements
have been made to the script to address various issues. Refer to the Fixed Issues section for
more information.
New firmware available for 5500 instruments
The firmware for the AB SCIEX QTRAP 5500 and AB SCIEX Triple Quad 5500 systems has
been upgraded. The new firmware addresses an issue where some mass spectrometers would
reset if the acquisition queue was aborted while the system was in the equilibration state. There
are no changes that affect data or data quality. For information on how to upgrade the firmware of
your mass spectrometer, refer to the Installation Guide for the Analyst 1.6.1 software.
Documentation Changes
Combined Hardware- and Software-Specific Information for 4500 Series of
Instruments into a Single Guide
All the hardware- and software-specific information for the 4500 series of instruments has been
combined into a single guide called the 4500 Series of Instruments System User Guide. The
guide also contains basic information for setting up and using the Analyst software to create
methods, acquire samples, and analyze data. This System User Guide replaces the Getting
Started Guide for the 4500 series of instruments. The Getting Started Guide is still applicable to
instruments other than the 4500 series of instruments.
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
Advanced User Guide
A new guide called the Advanced User Guide has been created. It contains all the advanced
information needed to set up and use the Analyst software to create methods, acquire samples
and analyze data. This guide replaces the Software Reference Guide.
Updated Reference Tables
The calibration reference tables have been updated in the Analyst 1.6.1 software. The changes
are only applicable to the 4000 and 4500 series of instruments. Existing calibration reference
tables will not be updated.
When installing a new 4500 series instrument, the FSE will install the new calibration reference
tables.
Fixed Issues
Corrected MRM Optimization script issue on the Windows 7 operating system
Occasionally when running the MRM Optimization script on the Windows 7 operating system, the
script would stop responding during the optimization process. This issue has been fixed and the
script now runs to completion. (TT 33878)
Unable to extract Multiple XICs to stacked panes
In the Analyst 1.6 software, if users attempted to extract multiple ion chromatograms to individual
panes, only one pane would contain an XIC; the rest would be blank. This issue has been
corrected and the Extract XIC functionality has been restored. (TT 34196)
Method duration may be calculated incorrectly
When calculating the expected duration of multi-period mass spectrometer acquisitions or
acquisitions with polarity switching, there may have been a mismatch between the calculated
number of cycles and method duration. As a result, acquisitions may have appeared to end early.
There was no data lost as the number of cycles acquired was correct — the defect was graphical.
This has been corrected and the expected duration now matches the calculated number of
cycles. (TT 34541)
Method Converter
Several defect fixes have been implemented in the Method Converter script for the Analyst 1.6.1
software:
•
Users were unable to convert AB SCIEX Triple Quad™ 5500 system methods to the
API 4000™ or API 5000™ system methods.(TT 34543)
•
Various user interface corrections, such as spelling, punctuation, and so on.
•
When converting MCA methods, the “Number of Scans to Sum” parameter was not
transferred to the converted method. (TT 34788)
Column Oven Parameters Help topic updated
The Analyst Help topic for Column Oven Parameters has been updated for clarity. (TT 34730)
Analyst® 1.6.2 Software
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Release Notes
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Enhancements and Fixes
Maximum/Minimum DP values for the 5500 instruments in Compound Optimization
was showing +/- 400 instead of +/- 300
When running the Compound Optimization routine, the reports were incorrectly showing the
Declustering Potential (DP) for the 5500 series of instruments as +/- 400 instead of +/- 300. This
issue has been corrected and the limits now show properly. (TT 34909)
No message displayed for source change when method editor active
The Analyst 1.6 software introduced a change that inadvertently removed the user message
when the source was removed or replaced while an acquisition method was open. This issue has
been addressed, and users will again see a message if the source is removed. (TT 34919)
Scheduled MRM™ Algorithm: Unable to save method if RT < Half Detection
Window
The Analyst 1.6 software introduced a requirement that retention times for ions in Scheduled
MRM™ algorithm methods had to be less than half of the user-set detection window. In response
to customer feedback, this limitation has been removed. (TT 35095)
Text in Current Spectrum window may overlap in Instrument Optimization
When running Instrument Optimization, users may have seen overlapping text in the Current
Spectrum window. This has been resolved. (TT 35177)
Agilent 1260/1290 DAD: Data mismatch with Agilent Instant Pilot
Recent firmware changes by Agilent have modified the scale used for absorbance data sent from
the Agilent 1260 and 1290 DADs to the Analyst software. As a result, users may have seen a
mismatch between the data shown in the Analyst software and the data shown on the Agilent
Instant Pilot. This has been corrected and features have been implemented to ensure that scale
changes will not affect the Analyst software data in the future. (TT 35191)
Note: The absorbance data as collected in the Analyst software was correct, but was
scaled improperly. Because DAD data is relative, the data was internally consistent.
New Enhancements and Fixes in Analyst 1.6
Software Components for 6500 Series
Instruments
New System Features
These features are in addition to the features and enhancements listed in the Analyst 1.6
software release notes.
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
Support for the 6500 Series Instruments
The Analyst 1.6 Software Components for 6500 Series Instruments adds support for the 6500
series of instruments, which can be used with or without SelexIon™ technology. The software
allows users to configure hardware profiles in two modes for each instrument:
•
Low mass mode, which provides high sensitivity within the 5 Da to 1250 Da range for
quadrupole scans and 50 Da to 1000 Da for LIT (linear ion trap) scans.
•
High mass mode, which expands the mass range to 5 Da to 2000 Da for quadrupole
scans and 50 Da to 2000 Da for LIT scans.
Configuring the mass mode to be used for acquisition
To activate a hardware profile for the 6500 series of instruments, the mass mode must first be
selected. This choice is located within the “Setup” page for the 6500 series of instruments. When
configuring a hardware profile, select the mass spectrometer and then click “Setup Device” to
open the configuration page. Use the Dual Mass Mode options located at the bottom of the dialog
to select the mass mode.
Note: Users should create two hardware profiles for the mass spectrometer — one for
high mass mode and the other for low mass mode. This will help to avoid inadvertently
submitting methods for a mass mode that is different from the activated hardware
profile.
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Release Notes
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Enhancements and Fixes
Note: Users are unable to submit acquisition methods that do not match the currently
configured mass mode. If the user attempts to submit a method that does not match the
currently configured mass mode, on clicking the Submit tab, the user is presented with a
message stating that the method is incompatible with the currently configured mass
mode. Also, the Submit button is not active. Submission of the method will not be
allowed.
Note: The Calibration Peak List for a low mass hardware profile for a 6500 series
instrument displays some additional ions that exceed 1000 Da for the quadrupole mode
or 1250 Da for the LIT mode (to view the calibration peak list, right-click in an open data
file, click List Data, and then click Peak List tab). For example, in the case of PPG
positive, the Calibration Peak List for a low mass hardware profile displays 1254, 1545,
and 1952 masses. The presence of additional ions in the list does not affect the actual
mass calibration of the instrument, and the additional ions are only displayed in the
Calibration Peak List. The workflows for Reference tables in Calibrate from Spectrum
and Tuning Options do not show additional ions in the low mass mode.
Mass Mode is visible within the Analyst Software
After a hardware profile is activated, the mass mode of a 6500 series of instrument is visible to
users from within the Analyst software. The Status display in the software has been updated to
show the active mass mode, and the File Information section of acquired data files will also show
which mass mode was used to acquire the data.
Support for SelexION™ Technology
The SelexION technology can be used with the 6500 series of instruments. The SelexION
technology allows the user to:
•
Control and monitor all DMS-related parameters from within the Analyst software.
•
Perform Compound Optimization for DMS parameters.
•
Separate isobaric compounds using DMS technology.
•
Use DMS parameters in IDA methods, including ramping Compensation Voltages.
For more information, refer to the SelexION Technology User Guide.
Method Converter updated for 6500 Series Instruments
The Convert Methods script has been updated to allow conversion of existing methods to be
used with the 6500 series of instruments. However, the Convert Methods script does not allow
conversion of existing methods with mass ranges over 1250 Da into a type that is compatible
with the low mass range 6500 series of instruments. In this case, the Save button in the script will
not be active.
Support for the IonDrive™ Turbo V Source
The 6500 Series instruments support the IonDrive™ Turbo V ion source. The source information
will be visible in the Instrument Status window.
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
MS3 scan type updated for 6500 Series Instruments
MS3 scan type has been updated for the 6500 series of instruments. The overall scan time for a
mass range will be significantly shorter than on the 5500 series of instruments, which will result in
more data points being acquired over the duration of the method acquisition.
New AAO interfaces added
The Analyst 1.6 Software Components for 6500 Series Instruments adds two new AAO
interfaces, to allow add-on applications to access features associated with the new mass modes
provided for the 6500 Series instruments. Refer to the AAO Release Notes and AAO User Guide
for more information.
Shimadzu SIL-30ACMP and CTO-30AS
The Analyst 1.6.1 software adds support for the Shimadzu SIL-30ACMP autosampler and CTO30AS column oven.
Documentation Changes
Combined Hardware- and Software-Specific Information for 6500 Series of Instruments
into a Single Guide
All the hardware- and software-specific information for the 6500 series of instruments has been
combined into a single guide called the 6500 Series of Instruments System User Guide. The
guide also contains basic information for setting up and using the Analyst software to create
methods, acquire samples, and analyze data. This System User Guide replaces the Getting
Started Guide for the 6500 series of instruments. The Getting Started Guide is still applicable to
instruments other than the 6500 series of instruments.
Advanced User Guide
A new guide called the Advanced User Guide has been created. It contains all the advanced
information needed to set up and use the Analyst software to create methods, acquire samples
and analyze data.
Fixed Issues
Change to Quantitation Fix introduced in Analyst 1.5.2 HotFixes to February 2011
software
In the Analyst 1.5.2 HotFixes to February 2011 software, a fix was introduced to allow the use of
the Sum Multiple Ions feature with compressed data. This fix has been improved upon. This
change has no effect on quantitation results. (TT 31956)
Improved support for Agilent 1260 DAD
The Agilent 1260 G4212B DAD was introduced in the Analyst 1.5.2 software. However, users
were not able to reliably activate the device or use it for acquisitions. This issue has been fixed.
(TT 33318)
Shimadzu Nexera POST treatment is now supported
In the Analyst 1.6 software, it was recommended to make sure that post-injection wash cycles
were completed before the end of the mass spectrometer acquisition to avoid errors. The Analyst
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Release Notes
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Enhancements and Fixes
1.6 Software Components for 6500 Series Instruments allows users to use post-injection wash
cycles of any length with the Shimadzu Nexera devices. Wash cycles no longer need to be
completed before the end of acquisition. (TT 33825)
Known Issues and Limitations
These issues are in addition to the known issues and limitations listed in the Analyst 1.6 Software
Release Notes.
Users should deactivate the hardware profile before turning the SelexION
controller module on or off
If users want to turn the SelexION controller module on or off (to temporarily add or remove the
SelexION technology to or from the system), first deactivate the currently active hardware profile
in the Analyst software. Failure to do so may result in the mass spectrometer entering an
unstable state resulting in a loss of control from the Analyst software. If the user does not
deactivate the profile and the mass spectrometer enters this unstable state, control may be
recovered by removing and re-seating the ion source, or by power cycling both the mass
spectrometer and the controller module and then reactivating the hardware profile. (ST 34011)
Using multiple DT values in a single acquisition method
When creating acquisition methods in which DT (DMS Temperature) is specified, users should
refrain from using different DT values between experiments and periods. While the DMS
technology is able to change DT during acquisition of a single sample, the system (mass
spectrometer and DMS technology) requires approximately 10 minutes to equilibrate before
collecting consistent data. Therefore, changing DT during a scan may lead to incorrect or
inconsistent data. (ST 33961)
Changing DT value in Manual Tuning
While in the Manual Tuning mode, if the user changes DT between scans, they should allow
approximately 10 minutes for the system (mass spectrometer and DMS technology) to
equilibrate before collecting consistent data.
Applying all DMS parameters to all experiments in Method Editor
When creating an acquisition method, if users want to apply their currently set DMS parameters
to all experiments of the same polarity, they do so by clicking Edit Parameters and then selecting
the options to apply the Source/Gas and Compound parameters to all other experiments of the
same polarity. Alternately, to apply only a subset, they can select either the Source/Gas or the
Compound option as listed in Table 2-1. (ST 33411)
Table 2-1 DMS parameters and their respective groups
Parameter name
Group
Separation Voltage (SV)
Compound
Compensation Voltage (COV)
Compound
DMS Offset (DMO)
Compound
DMS Resolution Enhancement (DR)
Source/Gas
DMS Temperature (DT)
Source/Gas
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
Table 2-1 DMS parameters and their respective groups
Parameter name
Group
Modifier (MD)
Source/Gas
Modifier Composition (MDC)
Source/Gas
Modifier Density (MDD)
Source/Gas
Modifier MW (MDW)
Source/Gas
Ramping COV in Method Editor
When creating an acquisition method with the Ramp COV option enabled, users will see that the
COV value is still editable in the Parameter Table. Editing this field will not affect the COV Ramp.
However, the value in this field will be displayed in the File Info. (ST 33573)
Ramping DMS parameters in Manual Tuning
When using the Ramp Parameter option in Manual Tuning and choosing to ramp a DMS
parameter (COV, DMO, or SV), users will see that the selected parameter is still editable under
the DMS Tab. Editing the value in the tab will not affect the selected ramp. This behavior is
consistent with other rampable Compound parameters. (ST 33573)
Indexes shown in Compound Optimization (FIA) may be incorrect
When running FIA Compound Optimization, on the Source Parameters window, users may see
that the indexes shown for Parameters do not progress linearly. This is because the DMS
parameters that cannot be optimized in the FIA workflow are hidden from view and the list is not
indexed again. (ST 33950)
Inaccurate error message if DMS controller box changes state during acquisition
If the DMS controller box is turned on or off during acquisition to a state that does not match the
method being acquired, the acquiring sample is aborted with the reason given as “stopped by
user.” (ST 35133)
Peak Hopping scans should not be used with the 6500 Series Instruments
The Analyst 1.6 Software Components for 6500 Series Instruments has not been optimized for
peak hopping scans with the 6500 series instruments. As a result, users should not use this scan
type with the 6500 Series Instruments. (ST 35863)
Convert Methods script incorrectly truncates masses to 1250 Da for LIT scans
When using the Convert Methods script to convert a method with a mass range above 1000 Da
(for example, a High Mass QTRAP 6500 method) for the QTRAP 6500 instrument when
operating in Low Mass mode, the script will incorrectly truncate the mass range to 1250 Da.
However, the Save button will be unavailable, so methods cannot be incorrectly saved.
(ST 36069)
Compound Optimization allows gradient methods to be used with Shimadzu LC
devices
When running Compound Optimization, the software cannot detect if a Shimadzu LC method is
isocratic. As Compound Optimization is only possible with isocratic methods, users should make
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Release Notes
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Enhancements and Fixes
sure that the starter method uses an isocratic flow when a Shimadzu LC stack is used.
(ST 36322)
When running Instrument Optimization, the final graph will not be displayed
When running Instrument Optimization, the on-screen graphs will show the results of the scan
that has just completed. However, after the final scan completes, the Optimization Report will be
shown, skipping the final graph. If Instrument Optimization is then executed immediately again,
the missed graph will be shown on-screen during the first scan. This a graphical issue only, and
optimization is not affected by this behavior. (ST 36328)
Guidance on using Reporter 3.2 with Library Search templates
If you are planning to use the Library Search templates in the Reporter 3.2 software to generate
reports, contact Technical Support using support@absciex.com. An action may be required on
the Dell OptiPlex 990 computers to enable these reports. (TT 36350)
Shimadzu autosampler state shows as green when a vial is missing
If a missing vial is detected during acquisition, the Analyst software will continue to display the
green Ready state for the Shimadzu stack, instead of showing red. However, the detailed status
for the stack does show that the autosampler has encountered a missing vial, and the event log
records the same warning. (TT 36339)
Compound optimization report cannot be saved properly in .pdf format
Users should refrain from saving Compound Optimization reports in .pdf format. Selecting this
option will product blank reports. (TT 36232)
Syringe pump button name in Manual Tune updates slower than usual
In Manual Tune, when the Start Syringe Pump button is clicked, occasionally the button name
does not update to “Stop Syringe Pump” in real time. This may cause the user to click the button
again, not realizing that the syringe pump has already started running. (TT 35711)
Graph Information Window is grayed out after more than one peak is highlighted
When the data being acquired in Manual Tune is viewed using the View > Graph Information
Window menu item and the user resizes the Graph Information window, then this window
becomes non-active and cannot be enabled. (TT 36158)
EPI method with CES enabled acquires longer than the set duration time
When an EPI method with enabled Collision Energy Spread (CES) and set method duration is
used to acquire data in manual tune, the data is acquired longer than the set duration time.
(TT 36079)
New Enhancements and Fixes in Analyst 1.6
Software
•
Analyst® software splash screens and icons have been updated.
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
•
•
•
Introduces support for Windows 7 (Professional Edition)
•
For users with Administrator privileges (Built-in Administrator or Protected
Administrator Users), the following UAC level is recommended: “Default –
Notify me only when programs try to make changes to my computer”.
•
For users without Administrator privileges (Standard Users), the following
UAC level is recommended: “Default – Always notify me when”.
•
Added the ability to pin both the AnalystLauncher and Analyst software
shortcuts to the Task bar. The shortcuts are consolidated into one button that
launches the Analyst software.
•
Ability for the Analyst software to track recently or frequently used files using
the Windows 7 jump list feature.
Enhancements for methods using the Scheduled MRM™ algorithm
•
Two Scheduled MRM algorithm experiments are now supported within a
single acquisition method.
•
IDA acquisition methods can now include two Scheduled MRM algorithm
experiments.
•
Introduces the ability to switch polarity during cycles that contain two
Scheduled MRM algorithm experiments.
•
The 5500 series of instruments now supports the acquisition of 4000
Scheduled MRM algorithm transitions with four parameters (CE, DP, EP,
CXP).
•
Scheduled MRM algorithm data containing more than 2500 transitions will be
opened in TIC mode.
Reporter 3.2 software is included with the Analyst 1.6 software
•
Reporter 3.2 software is now automatically installed during the installation of
the Analyst software.
•
Users can edit the Reporter 3.2 templates found in the <drive>:\Analyst
Data\Projects\API Instrument\Templates folder. User-created templates that
were created using previous versions of the Reporter software must be
updated using the Reporter Template Converter.
•
Analyst software now supports CTC firmware version 4.2.
•
Increased the mass range of the 3200 QTRAP® system to 2000 Da in RFDC mode.
LIT scan types are still limited to 1700 Da. A new configuration file for the 3200
QTRAP system is included. To use the increased mass range, the configuration
table must be updated using the ConfigUpdater.
New firmware for 5500 instruments is included
This firmware allows users to ramp the collision energy parameter using the CE values in the
mass ranges table. (ST 29645)
Analyst Access Object subproject support
The Analyst Access Object supports projects that use subprojects. (ST 16999)
Analyst® 1.6.2 Software
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Release Notes
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Enhancements and Fixes
User-created audit map enhancements
You can now delete the Default audit map and select a user-created audit map that will be
applied automatically when a new project is created. (ST 18933)
Users with the Administrator role can unlock the software
Users that have the Administrator role for the Analyst software can now unlock the Analyst
software if the application is locked by the current user. (ST 27692)
Users can print Results Tables that have been changed but not saved
If users modified the peak review layout and attempted to print the Results Table without first
saving it, they were prompted with a message stating that the Results Table has to be saved.
This issue has been corrected and users can now print the Results Table after the peak review
layout has been changed but not saved. (ST 27869)
Files in Cache folder are deleted
If you have confirmed that all data has successfully been uploaded to the server and files still
remain in the cache folder, restart the PC, navigate to \Analyst Data\WIFF_CACHE_BACKUP
(hidden folder) and delete the contents before re-launching the Analyst software. This issue has
been corrected. After network acquisition during which one sample file is saved per .wiff file has
completed, the files in the Cache folder are now deleted. (ST 28260, ST 28323)
Acquiring data to a network location does not clear temporary (Cache) files
When using Network Acquisition, the local cache folder may not be emptied after successfully
uploading the data file to the network. If this happens, users may see that the “Date Modified”
date for some data (.wiff) files in Windows has changed to a more recent time than when the file
was actually acquired. While the Windows timestamp of the file has been changed, the actual
contents of the file are not modified, unless there are actual changes to the data file that have not
yet been uploaded to the network.
Mapped drives are converted automatically
Previously network acquisition over mapped drives was not recommended. Now mapped drives
are converted automatically to full UNC paths. Full network path lengths must be limited to 128
characters. (ST 29237)
Audit Trail Manager logs invalid checksum
If Data File Checksum is activated, at the end of batch acquisition, the Audit Trail Manager now
logs any invalid checksum. (ST 31209)
Data discrepancy in quantitation
When performing an integration using the Analyst Classic algorithm, a discrepancy between the
chromatogram in the peak review and the Results Table is observed if the sample is corrupted.
The remaining samples were integrated incorrectly. This issue has been corrected. (ST 16964)
Unable to open Wiff to MatLab files generated using the Analyst 1.5 software
Files generated using the Wiff to MatLab script and Analyst 1.5 software data cannot be opened
in later versions of the Analyst software. This issue has been corrected. (ST 21099)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
During infusion Compound Optimization on the 5500 series of instruments, the
preset syringe pump options are used
Previously, during infusion Compound Optimization, the preset syringe pump options were used;
the syringe pump diameter and flow rate used were 4.61 mm and 7µL/min respectively and could
not be changed. To use a different syringe pump diameter, start the syringe pump in Manual
Tuning and then start Compound Optimization. (ST 9255, 24334)
Custom Injection program does not work for Agilent autosamplers
Previously, users could only create a basic custom injection program. This issue has been
corrected and users can now also create a custom injection program. (ST 31036)
Data acquisition using DFT occasionally results in a loss of sensitivity during
some DFT-enabled scans
When acquiring data using Dynamic Fill Time (DFT), in some rare instances users may
experience a loss of sensitivity during some DFT-enabled scans. When viewing the DFT Tracker,
they will also see that negative fill times are occasionally calculated during these scans. This
issue has been corrected. (ST 29880)
Shimadzu software stops responding during sample acquisition
The software stops responding during sample acquisition, either in pre- or post-run. This issue
has been corrected. (ST 29804)
Analyst® 1.5.1 Patch for AAO Batches
This patch corrects an issue found in the Analyst 1.5.1 software that prevents users from using
the Quantitation option available within the Batch Editor when the selected quantitation method
contains more than 150 transitions and control of any LC device is established through AAO
(Analyst Access Objects). In this scenario, attempting to acquire the batch results in failed
acquisitions. This patch functionality is included in the software.
Analyst® 1.5.1 Patch for DiscoveryQuant™ Software
This patch corrects the following issue: DiscoveryQuant — Optimize 2.1 software is not able to
successfully process certain product ion spectra (CE), and returns the error—2147467259 to the
user. The issue occurs randomly and is not always for the same sample. This patch functionality
is included in the software.
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Enhancements and Fixes
New Enhancements and Fixes in the Analyst
1.5.2 Software with HotFixes to February 2011
AAO and Companion Software
ChemoView Software Reports with large numbers of samples would intermittently
fail
When using the ChemoView™ software to create reports with large numbers of samples, users
would intermittently see reporting fail for some samples. This was only seen for large (typically
over 100 samples) report batches, and re-running the report would often work properly. This has
been corrected. (ST 24863)
Submission of a batch fails if the user selects a Quantitation method with more
than 150 transitions
When creating an acquisition batch through an AAO application, if the user selected a
Quantitation method with more than 150 transitions, the batch submission would fail. This has
been corrected. (ST 21398)
Reporter 3.0.1 Software Integrated into the Analyst Software Installer
Previously, the Reporter 1.0 software was installed by default, and the Reporter 3.0.1 software
was included in the installation DVD as an optional software. The Reporter 3.0.1 software is now
integrated into the Analyst 1.5.2 Software with HotFixes to February 2011 and installed along with
this software. If users have older Reporter 1.0 reports and wish to use them with the Reporter
3.0.1 software, there is a conversion utility available from Start > Programs > AB SCIEX >
Reporter 3.0.1. (ST 24738)
Note: If the standalone Reporter 2.0 software is installed on the computer, it should be
uninstalled before installing the Analyst 1.5.2 Software with HotFixes to February 2011.
If the Reporter 3.x software is installed on the computer, it will be automatically removed
and replaced with the integrated Reporter 3.0.1 Software during the installation of the
Analyst 1.5.2 Software with HotFixes to February 2011. Any custom queries and
templates will be preserved. If a default query has been modified, a new unmodified
version will also be installed with the suffix “_new”.
Note: If the standalone Reporter (2.0 or 3.x) software is installed after installing the
Analyst 1.5.2 Software with HotfFixes to February 2011 and is later uninstalled, the
Analyst 1.5.2 Software with HotfFixes to February 2011 may lose reporting capabilities.
In this scenario, the Analyst 1.5.2 Software with HotfFixes to February 2011 should be
reinstalled.
Users were required to log-in twice when using certain Companion Software
When a user logged into the Analyst software with Mixed Mode security enabled and then
launched certain companion software (for example, MPX™ driver software), they may have been
required to enter their logon credentials when launching the Analyst software as well as when
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
launching the companion software. This has been changed, and users will be required to provide
their credentials only upon launching the Analyst software. (ST 25713)
DiscoveryQuant — Optimize software would fail during acquisition
When using the DiscoveryQuant™ — Optimize software, data acquisition would fail for certain
samples and report the error - 2147467259. The Analyst software has been corrected to prevent
this issue from occurring in future versions of the DiscoveryQuant — Optimize software that
support the Analyst 1.5.2 Software with HotFixes to February 2011. (ST 26055)
Acquire — Acquisition and Batch Editor
Some Scheduled MRM algorithm scans would result in lower intensities than the
corresponding MRM scans
In rare situations, users would see that a Scheduled MRM algorithm scan would show lower
intensities than the corresponding MRM scan if the line obtained by plotting Resolution offsets
against Mass passed through (or near to) the origin. This has been corrected, and now the
corresponding Scheduled MRM algorithm scans will show proper intensities. (ST 24728)
Configure — Hardware Configuration
Included support for the following Agilent 1260 devices (ST 24294):
•
G1310B Isocratic Pump
•
G1311B Quaternary Pump
•
G1312B Binary Pump
•
G1316A Thermostatted Column Compartment (TCC)
•
G1367E Autosampler
•
G4212B Diode Array Detector (DAD)
Included Support for the following Agilent 1290 devices (ST 25922):
•
G4220A Binary Pump
•
G4226A Autosampler
•
G4212A Diode Array Detector (DAD)
•
G1316C Thermostatted Column Compartment (TCC)
Added support for barcode reading with CTC PAL autosamplers
Users are now able to enable or disable reading and recording the barcode information on vial
labels during acquisition, when using a CTC PAL autosampler that supports this feature. The
information will be stored and visible in the data file (File Info). Also, when data containing
scanned barcodes is quantitated, a “Scanned Barcode” column will automatically be added to the
Results Table. (ST 26786)
Analyst® 1.6.2 Software
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Release Notes
RUO-IDV-03-0236-A
Enhancements and Fixes
RFID tags supported for 1290 TCC switching valve
The Agilent 1290 TCC (G1316C) supports switching valves with RFID tag. When data is acquired
with an RFID tagged switching valve, the valve type and serial number will be added to the File
Info of the sample.
RFID tags supported for DAD Flow Cell and Lamp
The Agilent 1290 DAD (G4212A) supports RFID-tagged flow cells and lamps. When data is
acquired using an RFID tagged flow cell or lamp, the serial number of the part will be added to
the File Info of the sample.
Analyst 1.5.2 Software with HotFixes to February 2011 supports the most recent
Agilent devices firmware
The Analyst 1.5.2 Software with HotFixes to February 2011 has been tested with the latest (at
time of release) released firmware versions for supported 1100, 1200, 1260 and 1290 devices.
For a list of supported firmware, see the Software Installation Guide for the Analyst software.
Explore
The Calibration Tables timestamp shown in File Info may be incorrect if a non-US
time format is used
If data was acquired on a computer using a non-US date format, and if the users view the File
Information on a different computer, they might see that the “Last Modification Date” for the
Calibration Tables was the same as the Sample Acquisition timestamp. This has been corrected,
and the data acquired on a computer using a non-US date format will display the correct
timestamp for the Calibration Tables’ Last Modification Date. (ST 22722)
Checksum Verification may fail even though the data file is intact and not
corrupted
In rare instances, when verifying the Checksum information embedded within a .Wiff file, the
Analyst software would incorrectly report that the verification had failed. The Analyst 1.5.2
Software with HotFixes to February 2011 corrects this issue and will now correctly report that the
verification has succeeded when the data is intact. This does not affect the verification results of
corrupted/modified files, which will continue to fail checksum verification. (ST 26701)
Explore — Library Search
Printed Library Search results do not match the on-screen results
When printing the results of library searches, users would see the following formatting errors in
the printed output: the font size of the printed text would be too large; in single-page printing, the
second library match would always be printed even when not requested; and in multi-page
printing, UV spectra would not be printed even when requested. The Library Search printing
functionality now works properly; the text is printed in a reasonable font size, and only the
requested elements are printed. (ST 23330)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
Firmware Files
New firmware available for AB SCIEX QTRAP 5500 and AB SCIEX Triple Quad 5500
systems
The firmware for the AB SCIEX QTRAP® 5500 and AB SCIEX Triple Quad™ 5500 systems has
been upgraded. The changes made in this firmware revision are not customer facing. For
information on how to upgrade the firmware of your mass spectrometer, see the Software
Installation Guide for the Analyst software.
Help Files and Tutorials
Contents of Ion Optics Tutorial revised
The Ion Optics Tutorial (available at Start > Programs > AB SCIEX > Analyst > Tutorials) has
been revised for content and accuracy. (ST 25565)
“Library Search Results” Help topic updated
The topic “Search Results: Print Options Dialog” has been updated to more accurately reflect the
various printing options. (ST 28211)
Obsoleted Help files removed
Two help files, ENDURANCEAS.hlp and PALAS.hlp are no longer required and have been
removed from the \Program Files\Analyst\Help folder. (ST 23351)
Quantitate
Quantitation fix to prevent rounding errors with IntelliQuan Algorithm (addendum
to fix in the Analyst 1.4.2 software)
In the Analyst 1.4.2 software, a change was implemented for the IntelliQuan algorithm to reduce
the likelihood of rounding errors causing a discrepancy between the Results Table and Peak
Review due to an improper selection of the Noise Threshold. The Analyst 1.5.2 Software with
HotFixes to February 2011 builds upon this fix by further reducing the likelihood of these
discrepancies being created. The IntelliQuan algorithm has not been changed. (ST 27614)
Quantitation fix to prevent rounding errors with Analyst Classic Algorithm
When using the Analyst Classic algorithm to create Results Tables, there was a rare possibility
that users might see a discrepancy between the values shown in the Results Table and in Peak
Review. Depending on the Peak Separation Width selected, a small rounding error could affect
the baseline calculation and cause the Peak Review pane to calculate areas differently than in
the Results Table. The likelihood of users experiencing this discrepancy has been significantly
reduced without changing the Analyst Classic algorithm. (ST 21863)
Note: For details on the original solution implemented in the Analyst 1.4.2 software,
see Appendix B (reprinted from the Analyst 1.4.2 Software Release Notes).
Analyst® 1.6.2 Software
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Release Notes
RUO-IDV-03-0236-A
Enhancements and Fixes
Record Modified flag stays on even though the entire quantitation method was
updated
If the user changed some integration parameters in Peak Review and then selected the option to
Update the Method, the Record Modified flag would not always be cleared for the updated peaks.
This has been corrected and the Record Modified flag will now be cleared when the method is
updated. (ST 26582)
Sum Multiple Ions may produce incorrect results
Previously, when the Sum Multiple Ions option was used to create a quantitation method, the
Results Tables produced with this method may have shown visible artifacts when the peaks were
viewed in Peak Review. This issue has been corrected. (ST 21831)
Accept Changes dialog may not be shown for manual integrations
If the user performed a manual integration in Peak Review and navigated to a different sample or
the Results Table, they may not have been prompted to accept the change before it was
committed. This has been corrected, and the Accept Changes dialog will be displayed when
navigating away from an uncommitted change. If the Audit Map is configured to require either a
Reason or E-Signature for a manual integration, the Accept Changes dialog will not be presented
to the user. (ST 22745)
Scripts
MRM3 Optimization Script replaces MS3 Quant Optimization script and is installed
by default
The MS3 Quant Optimization script has been replaced by the MRM3 Optimization Script. This
script provides the functionality of the MS3 Quant Optimization script and adds the ability to work
with peptides and multiple charged ions. Users who upgrade from a previous version of the
Analyst software will retain the previous MS3 Quant Optimization script and also receive the new
MRM3 Optimization script. Users who perform a fresh installation of the Analyst software will see
only the MRM3 Optimization Script in the Script menu within the Analyst software. (ST 22752)
Program Shortcuts
New documentation is available in Start > Programs > AB SCIEX > Analyst > Site
Planning Guides
•
API 2000™ System Site Planning Guide
New documentation is available in Start > Programs > AB SCIEX > Analyst >
Qualified Maintenance Guides
•
API 2000™ Qualified Maintenance Guide
New documentation available in Start > Programs > AB SCIEX > Analyst > Ion
Source Guides
•
Turbo V™ Ion Source Operator’s Guide
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
•
NanoSpray® Ion Source Operator’s Guide
•
DuoSpray™ Ion Source Operator’s Guide
•
API 2000™ Source Operator’s Guide
•
NanoSpray III Head and Emitter Tip Assembly
•
PhotoSpray® Ion Source Operator’s Guide
•
Ion Source Specifications
Device Support
Support for Agilent G1367D Autosampler
Analyst® 1.5.1 HotFixes to June 2010 adds support for the Agilent 1367D model Autosampler.
(ST 18976)
Support for Agilent 1200 G1329B Autosampler
Analyst® 1.5.1 HotFixes to June 2010 adds support for the Agilent 1200 1329B model
Autosampler. (ST 18976)
New Enhancements and Fixes in the Analyst
1.5.1 HotFix
Note: For reference, the name of the software patch or HotFixes release where the
issue was previously fixed is included.
Acquire
Default scan speed for ER scans on the 3200 QTRAP system changed to 1000
amu/s
The default scan speed for ER (Enhanced Resolution) scans on the 3200 QTRAP system has
been changed to 1,000 amu/s. The option for 250 Da/s still exists and can be selected by users
who want to use the slower speed. (ST 21519)
Quantitate
Prevent exporting or saving Results Tables containing unsaved changes
Users will now be forced to save a results table before they export or print from it. This new
workflow feature is designed to help customers adhere to operating procedures that prohibit the
practice of printing or exporting unsaved results tables. However, it remains the responsibility of
the customer to ensure that SOPs are created and followed to prevent users from taking actions
in the software that may be possible, but not desirable. (ST 19788)
Analyst® 1.6.2 Software
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Release Notes
RUO-IDV-03-0236-A
Enhancements and Fixes
Security
Project Level Security enhancement when using AAC
Analyst 1.5.1 software introduced changes to the way in which project-level security is managed
when using AAC (Analyst Administrator Console). The Analyst® HotFixes to June 2010
introduces the ability for users to choose between strict project-level control (as in Analyst 1.5.1
software) and the previous (pre-1.5.1) project-level control. Administrators have the option to
enable or disable enhanced project-level security on a client-by-client basis, allowing some users
to operate in a relaxed environment while tightly controlling the project-level security of other
users. No changes were made to the AAC Server for this enhancement. (ST 20497)
Fixed Issues
Acquire
IDA Experiments with an ADC Card in the active hardware profile are now possible
If an ADC (Analog-Digital Conversion) card was active in the Hardware Profile, users were
unable to run IDA experiments. Doing so caused the ADC card to fail and turn red in the
Instrument Status area, which in turn caused the acquisition to fail. (ST 16102)
Users can now control Agilent 1100 or 1200 Hardware in a CAN configuration over
Ethernet
Users were unable to connect Agilent LC hardware in a CAN configuration if the first device was
connected to the computer via Ethernet. Users can now use both Ethernet and RS-232
connections for the first device in a CAN configuration. (ST 16108)
Peak Hopping scans missing first data point
When performing acquisitions using the Peak Hopping scan mode, the data list would begin
above the requested start mass. This has been corrected and when performing Peak Hopping
scans, users will see all non-zero data points. (ST 16866)
Mass Defect not applied uniformly during Peak Hopping scans
When performing acquisitions using the Peak Hopping scan mode, if the number of
measurements (or spectrum data points) was less than or equal to 97 users would see the
entered Mass Defect only applied to the first data point. Subsequent points would then be
incremented solely based on the step size. However, if the mass range was greater than 97 Da,
the Mass Defect would be applied correctly, but data points would be shifted as described above.
(ST 22642)
Dynamic Fill Time was occasionally calculated incorrectly for ER scans
When an ER scan using DFT was included in a method that uses LC, occasionally, the required
fill time was improperly estimated and defaulted to the maximum fill time value regardless of ion
intensities. This sometimes resulted in ER scans that were of poor spectral quality due to space
charge. This issue applied only to non-AB SCIEX QTRAP 5500 systems, but is now fixed.
(ST 17281)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
31 of 100
Enhancements and Fixes
IDA methods using two EMS scans of opposite polarities now properly triggers
dependent scans
If an IDA method contained two EMS survey scans of opposite polarities, the dependent scan
would not be triggered even if the IDA criteria were satisfied. (ST 17045)
Security
Analyst software now supports long domain names in Mixed Mode
If a network domain contained more than 15 characters, users were unable to use Audit Trails.
Users would find that upon entering their credentials for an e-signature, the password would be
rejected and an error message would be presented. (ST 20279)
Quantitate
Area Ratio columns containing Div/0! would be exported as “-7”
When exporting Results Tables to text files, if an Area Ratio column containing Div/0! entries was
exported, the Div/0! fields would be exported as “-7”. They will now be exported as “N/A”. (ST
18919)
Quantitation Methods with multiple decimal places may be modified if the user
switches between tabs
If the user was building or viewing a quantitation method that includes transitions specified to 2 or
3 decimal places, switching between the Components and Integration tabs in the full method
editor may have caused similar transitions to be modified or switched. Users would notice that
the decimal components of the transitions were rounded or changed upon returning to the
Components tab and the chromatograms may have become mismatched with their respective
analytes in the Integration tab. (ST 22277)
New Enhancements and Fixes for the Analyst
1.5.1 Software
Note: For reference, the name of the software patch or HotFixes release where the
issue was previously fixed is included.
Merged two software platforms into a single version of the software
This release combines the Analyst 1.5 software and the Analyst software 1.5 5500 Components,
providing one software version that supports all our currently supported QTRAP and triple
quadrupole instruments. For a list of supported instruments, see the Analyst® 1.5.1 Software
Installation Guide. In addition, previously released HotFixes and patches have been included.
Added support for the following Microsoft products
•
Microsoft Office 2007
Analyst® 1.6.2 Software
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Release Notes
RUO-IDV-03-0236-A
Enhancements and Fixes
•
Microsoft Windows XP SP3
New software and hardware documentation available
In Start > Programs > AB SCIEX, the following new documentation is available:
•
Standard Quantitation Tutorial
•
Hardware Guides for all systems
•
Safety Guides in the following languages: French, German, Italian, Japanese,
Spanish, and English
•
Protein and Peptide Quantitation Tutorial
•
Ion Optics Tutorial for the 5500 series of instruments
•
Qualified Maintenance Guides
•
Site Planning Guides
Integrated support for GPIB driver version 2.5
GPIB driver version 2.5, including USB.
Script enhancements
•
Improved IDA Trace Extractor script to allow the ability to select polarity per fragment
or neutral loss specified or fragment and neutral loss specified.
•
Improved Dynamic Background Subtraction™ (DBS) algorithm to add more control
over the DBS functionality embedded in methods created in the Analyst software.
Users now have access to the number of background spectra that they want to
average as well as access to the number of points for smoothing the current
spectrum.
•
Improved Merge MRM methods script to allow the option to populate the Compound
ID column in the final MRM method with the compound name used in Compound
Optimization.
•
Improved the Regression calculator by resizing the form, text boxes, and labels to
enable the display of values smaller than 0.001. (ST 16959)
•
Convert Methods script enhancements. The following Convert Methods script issues
have been fixed:
Release Notes
RUO-IDV-03-0236-A
•
Convert Methods script incorrectly converted Scheduled MRM algorithm
methods to MRM methods. This script now allows the user to automatically
carry over the retention time information and all other Scheduled MRM
parameters without having to enter them manually. (ST 15463)
•
The Compound IDs were not carried over to the newly created method when
running the Convert Methods script. The Compound IDs are now carried over
automatically. (ST 15464)
•
When users converted IDA methods, the IDA criteria and dependent scan
experiments were lost. This script now carries over the IDA Criteria and
dependent scans automatically. (ST 15326)
•
The Convert Methods script did not optimize the mass ranges for LIT scan
types when converting methods for use between QTRAP systems. This script
now automatically optimizes the mass ranges for the new method. (ST 18670)
Analyst® 1.6.2 Software
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Enhancements and Fixes
Configure — Hardware Configuration
Included support for the following Shimadzu devices for the 5500 series of
instruments
•
Included support for the Shimadzu High Pressure LC devices: LC-20ADXR pump
and the SIL-20ACXR and SIL-20AXR autosamplers. (ST 15748)
•
Integrated Shimadzu LC MIMIC 5.4 SP1 driver (version 5.4.1.7). (ST 17947)
Agilent 1200 DAD G1315 C and D models acquire at the set rate
Agilent 1200 DAD G1315 C and D models acquire at the set rate when in Spectral Mode. All
frequencies can be acquired now. (ST 12696)
A new entry has been added to the autosampler database to support the MPX™-2
High Throughput System
The autosampler database has been updated to include MPX-CTC as on option on the Location
tab in the Batch Editor. (ST 16742)
Invalid parameter Access Ranges are now corrected
After installing the Analyst® 1.5 HotFixes to March 2009, the parameter Access Ranges were
replaced by the firmware ranges, atypical behavior may have been observed and it may not have
been apparent that the parameter settings were the cause. Because the firmware range for each
parameter is typically much wider than the Access Range appearing in the originally installed
software, switching a positive mode polarity method to the negative mode polarity, or vice versa,
causes opposite polarity lens values to be applied and used in a method without any software
error messages appearing. Consequently, a user may not have been able to see any data being
collected when running such methods. During installation of the Analyst 1.5.1 software, these
ranges are checked and the user is prompted if they need correcting. (ST 15063) (Analyst® 1.5
Patch for ParamSettings Access Ranges.)
Acquire — Acquisition and Batch Editor
The Target Scan Time for 5500 systems is now optimized
The actual scan time calculated from the Target Scan Time in Scheduled MRM algorithm
experiments is now calculated differently for the 5500 systems because of the superior
performance of these systems. As a result, users may notice a decrease in the dwell time used in
their methods. Also, a greater number of MRM transitions in a single window can now be
acquired. (ST 13970)
Autosamplers are now automatically selected in the Select Autosampler dialog
Previously, users had to select the autosampler in the Select Autosampler dialog when they
imported a batch. Now when you import a batch, the autosampler that is automatically selected is
the same one used in the active hardware profile. (ST 15747)
Analyst® 1.6.2 Software
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Release Notes
RUO-IDV-03-0236-A
Enhancements and Fixes
Charge state now optimized when switching polarity at the dependent scan level
In previous Analyst software versions, when the charge state of a peak at the survey or
confirmation level was undetermined, the mass assignment for that peak was not changed as
expected in subsequent experiments. The polarity switching is now working correctly when
switching polarity at the dependent scan level in an IDA method regardless of the assigned
charge state for the survey peak. (ST 14702)
Improvements to the MS/MS/MS scan type for the 3200 QTRAP systems
Improved the intensity for MS/MS/MS scan types. Users may notice an increase of 30.5 ms in
their acquisition methods. (ST 17882)
Issue applying Source/Gas parameters to opposite polarity experiments in a single
method now corrected
If the acquisition method had two experiments with different polarities and the user applied
source and compound parameters to all other experiments, the Analyst software may have
stopped responding. This issue is now resolved. (SCR 14299)
Tune and Configure
DP values used during optimization are now within range
Instrument Optimization now addresses the issue where the DP values used during optimization
were out of range for some systems (API 5000™, AB SCIEX Triple Quad 5500, and AB SCIEX
QTRAP 5500 systems) causing Instrument Optimization to stall in some instances. For these
cases, optimization is expected be more successful. (ST 17937, ST 9982)
Quantitate
Quantitation methods distinguish between MRM transitions
The quantitation method now distinguishes between MRM transitions where masses are at least
0.001 Da apart. This limit was previously 0.1 Da. (ST 14231)
Compatible Software
Analyst software menu option and icon now automatically opens the Reporter
software
The Tools > Report menu option, including the icon in the tool bar, will open the Reporter
software found in the Companion Software section in the Navigation bar. (ST 15755)
Analyst Administrator Console support improvements
When users log on to the Analyst software, they will only see projects for which their workgroup
has access. Now users will be forced to re-authenticate their credentials if they change root
directories. As a result, users may not have access to local projects such as the API Instrument
project. These local projects must be shared and then added to Workgroups if access to these
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
folders is required at the Workgroup level. The local projects are still available when logging in
locally. (ST 14015)
Improvements to the Translate.exe utility
You can now translate NETCDF files to .wiff files and .wiff to NETCDF files for all data files. (ST
14018)
Audit Trail
Screen lock and auto logout Wait Times recorded correctly in the Audit Trail
Manager
The wait times for screen lock and auto logout were reversed in the Audit Trail records when the
features were enabled. These fields are now recorded correctly. (SCR 5014) (Analyst® 1.5
HotFixes to March 2009)
Actual Lockout and Auto Logout Wait times can be entered correctly
The actual Lockout and Auto Logout Wait times within the Security Configuration options were
reversed relative to the entered values. This issue has now been fixed. (Analyst® 1.5 HotFixes to
March 2009)
Acquire — Acquisition and Batch Editor
The mass range has been increased to 1250 Da for quadrupole scan types on the
5500 series of instruments
This change is for quadrupole scan types only (Neutral Loss, Precursor Ion, Product Ion, MRM,
Q1 MS, Q1 Multiple Ions, Q3 MS, Q3 Multiple Ions). The mass range for LIT scan types remains
at 50 to 1000 Da. (ST 13316) (Analyst® 1.5 Software Components for 5500 Systems HotFixes to
April 2009)
A new scan speed has been introduced for quadrupole scan types on the 5500
series of instruments
A new scan speed of 12000 Da/s is now available for the following scan types: Neutral Loss,
Precursor Ion, Product Ion, Q1 MS, Q3 MS. (ST 11711) (Analyst® 1.5 Software Components for
5500 Systems HotFixes to April 2009)
Mass range for the API 3200 LC/MS/MS System has been increased to 2000 Da
An updated Configuration Table is included for this enhancement. The feature is optional and will
not be activated until the updated Configuration Table (B9633002.FW) has been installed on the
API 3200™ instrument. This mass range extension only applies to the triple quadrupole system
and does not apply to the 3200 QTRAP system. (TT 10436) (Analyst® 1.5 HotFixes to March
2009)
Analyst® 1.6.2 Software
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Release Notes
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Enhancements and Fixes
The pause time is maintained for Q1, Q3, MS2, Precursor, and Neutral Loss scan
types for the API 5000™ system
The user can now toggle between tabs without the pause time doubling when the average mass
entered in the mass ranges table is equal to or exceeds 1000 Da. (ST 11465)
Diverter valve fixes
•
The diverter valve on the 5500 series of instruments now switches correctly in MS/
MS/MS experiments. (ST 14521) (Analyst® 1.5 5500 Components Patches - August
2009)
•
Acquisition is now successful when the diverter valve on a 5500 instrument is
included in a method containing a Scheduled MRM algorithm experiment type, when
the method is an IDA method, or if the acquisition method is being collected with
Dynamic Fill Time (DFT). (ST 13730) (Analyst® 1.5 5500 Components Patches August 2009)
•
Users can now switch the integrated diverter valve on a 5500 instrument when using
an LC stack during MRM acquisition. (ST 12157) (Analyst® 1.5 Software
Components for 5500 Systems HotFixes to April 2009)
•
Running a batch with over 200 samples will no longer cause the batch queue to stall
at about sample 210 when the acquisition method contains a diverter valve method
for the internal diverter valve on a 5500 instrument. (ST 17168) (Analyst® 1.5 5500
Components Patches - August 2009)
Support for new autosampler layouts
The Analyst software autosampler database has now been updated to support new autosampler
layouts from the device vendors: (Analyst® 1.5 HotFixes to March 2009)
•
Dionex TSP AS3000/AS3500 (SCR 15521)
•
Dionex ACC-3000 (SCR 15521)
•
Jasco AS-1555 (SCR 15522)
•
Jasco AS-1550 (SCR 15522)
•
Jasco AS-1559 / AS-2059 / AS-2059-SF / X-LC3059AS (SCR 15522)
•
Jasco AS-2050 / AS-2051 (SCR 15522)
•
Jasco AS 2055 / AS-2057 (SCR 15522)
•
Shimadzu: control rack for SIL-20A, 20AC, 20AXR, and 20ACXR (SCR 15319)
•
Waters Acquity (SCR 15524)
Sample peak in the MS no longer delayed when acquired with the Shimadzu UV
detector
When the Shimadzu UV detector was used in acquisition, the sample peak in the MS was
delayed 30 seconds even though no delay was specified. This issue has been fixed. The delay is
no longer observed. (SCR 15534) (Analyst® 1.5 HotFixes to March 2009) (ST 12316) (Analyst®
1.5 Software Components for 5500 Systems HotFixes to April 2009)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
Support for Shimadzu autosampler injection volumes of less than 1 µL
Acquisition methods with injection volumes down to 0.1 µL are now supported. Previously, users
could only use injection volumes equal to or greater than 1 µL. (ST 10763) (Analyst® 1.5
HotFixes to March 2009)
Included support for the following Shimadzu devices
Support for the Shimadzu High Pressure LC devices, LC-20ADXR pump and the SIL-20ACXR
and SIL-20AXR autosamplers, has been implemented for the following systems: 2000 series of
instruments, API 3000™ instrument, 3200 series of instruments, 4000 series of instruments, and
the API 5000 instrument. (ST 15748) (Analyst® 1.5 HotFixes to March 2009)
Autosampler name appears correctly in the Batch Editor Autosampler layout list
The LC Packings WPS-3000 autosampler now appears as Dionex WPS-3000. The autosampler
layout is correct and has not been changed. (SCR 15551) (Analyst® 1.5 HotFixes to March 2009)
Injection volume can now be entered in the Method Editor
In the Method Editor, when attempting to enter the injection volume for CTC PAL autosamplers,
users received an error for every digit they entered. Now users can enter the injection volume
without any errors. (ST 14016) (Analyst® 1.5 Patch for CTC PAL Autosampler Injection Volumes)
Batch submission speed increased when using multiple methods
Previously when using a CTC PAL autosampler, batches with multiple methods slowed the
submission speed of the batches. Batches using multiple methods submit successfully now with
no delays. (ST 14016) (Analyst® 1.5 Patch for CTC PAL Autosampler Injection Volumes)
All valid injection volumes can now be used with CTC autosamplers in both the
Method and Batch editors
With systems using the CTC PAL autosampler, when users attempted to enter an injection
volume in the Method and Batch editors, they received an error when trying to enter valid
volumes. All valid injection volumes can now be used in the Method and Batch editors. (ST
14016) (Analyst® 1.5 Patch for CTC PAL Autosampler Injection Volumes)
Injection volume now validates against specified syringe size for the CTC PAL
autosampler
The injection volume can now be validated against the installed syringe, and the selected method
syringe. (SCR 12931) (Analyst® 1.5 Patch for CTC PAL Autosampler Injection Volumes)
Acquire — Information Dependent Acquisition (IDA) and
IDA Method Wizard
Long IDA batches containing an ER scan type now acquire successfully
Long (about 25 hours) Information Dependent Acquisition (IDA) batches that contained an ER
scan type with DFT enabled are now acquired successfully. (ST 13718) (Analyst® 1.5 5500
Components Patches - August 2009)
Analyst® 1.6.2 Software
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Release Notes
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Enhancements and Fixes
Correction of calibration shifts
Calibration shifts of up to 1 Da or more were observed when two or more precursor ion scan
types, two neutral loss scan types, or a combination of these two scan types was used either
inside or outside an IDA experiment. This issue has now been fixed. (ST 12749) (Analyst® 1.5
5500 Components Patches - August 2009)
Correct DAC value applied for negative precursor ion scan type or neutral loss
scan type
If a user ran an experiment that contained a negative precursor ion scan type or a neutral loss
scan type, a calibration shift for the negative ions was observed. This issue has now been fixed.
(ST 13636) (Analyst® 1.5 Software Components for 5500 Systems HotFixes to April 2009)
Calibration shift no longer observed when looping two precursor ion or two
neutral loss experiments (or a combination of the two experiments)
If a user used any two precursor ion scans, two neutral loss scans, or a combination of those two
scan types, a calibration shift of approximately 1 Da was observed. This issue is now fixed. (ST
12749) (Analyst® 1.5 5500 Components Patches - August 2009)
Quantitate
All Results Tables from previous versions of the Analyst software open
successfully
If a user tried to open a Results Table created in a previous version of the Analyst software, the
software occasionally closed unexpectedly without logging any errors in the event log. This issue
did not affect data integrity. This issue has now been fixed. (ST 15562) (Analyst® 1.5 Software
Components for 5500 Systems HotFixes to April 2009) and (ST 12870) (Analyst® 1.5 HotFixes to
March 2009)
‘Apply to All Rows’ check box added to query for Results Tables
You now have the option of applying a query to only those rows that are currently visible in the
Results Table or to all the rows in the Results Table. To use this feature, select the Apply to All
Rows check box in the Query Editor dialog. (SCR 15543) (Analyst® 1.5 HotFixes to March 2009)
Nested queries and group/ungroup logic fixes added to Results Table queries
You can now group or ungroup queries. You can also nest queries within other queries as long as
they do not share the same start or end item. (SCR 15543) (Analyst® 1.5 HotFixes to March
2009)
‘One click’ peak review available in Calibration plot
You can now open the peak review pane by clicking a data point on the calibration plot. Click
another data point to refresh the peak review pane and show the peak associated with that point.
(SCR 15543) (Analyst® 1.5 HotFixes to March 2009)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
39 of 100
Enhancements and Fixes
Analyte names field expanded in the calibration pane
The Analyte list field containing the names in the calibration pane has been modified to allow for
a greater number of Analytes to be displayed. Previously, the box showed a maximum of three
analytes. (SCR 15543) (Analyst® 1.5 HotFixes to March 2009)
Filter Results Table by Sample Type now available
In addition to filtering the Results Table rows by Analyte and Analyte Group, you can now filter a
Results Table by Sample Type and view only a specific type at a time. (SCR 15543) (Analyst® 1.5
HotFixes to March 2009)
New ‘contains’ Operator for custom Formula column available
You can now create a formula for a custom Formula column in the Results Table using the new
“contains” operator. This operator performs a string comparison of two fields and then returns
either a TRUE value, if one string is contained within the other, or FALSE, if one string does not
contain the other.
The custom Formula column can then be queried to show only those that are TRUE or FALSE,
depending on preferences. (SCR 15543) (Analyst® 1.5 HotFixes to March 2009)
Expected Retention Time appears correctly in the Results Tables
If you used the Quantitation Wizard to create a new Results Table using the Automatic Method
option on the Select Method page, the Analyte Expected Retention Time was incorrectly reported
as “0” for the first compound and Expected Retention Time values were shifted to the next
compound. The Analyte Expected Retention Time is now correctly populated. (TT 9401)
(Analyst® 1.5 HotFixes to March 2009)
ADC data can be quantified by the Analyst Classic algorithm
When quantifying ADC data with the Analyst Classic algorithm, the user received the message
“The method cannot be used because it is not compatible with all of the selected samples.” You
can now quantitate ADC data using the Analyst Classic algorithm. (TT 6978) (Analyst® 1.5
HotFixes to March 2009)
Quick Quant method uses the customer-selected IntelliQuan values
After the preset parameters were modified using the IntelliQuan global settings, those preset
values were not used when creating Quantitation methods using the Quick Quant feature in the
Batch Editor. Instead, parameters in the Quantitation method creation dialog were reset to zero.
Now, the Quantitation methods using the Quick Quant feature in the Batch Editor use the preset
values that were set in the IntelliQuan dialog. (TT 6997) (Analyst® 1.5 HotFixes to March 2009)
IS Quality no longer displays unknown characters
When no peak was found, the IS Integration Quality in the Integration Quality displayed “-1.J#”
instead of the correct value of zero. Now, the IS Integration Quality reports correctly as zero. (TT
7388) (Analyst® 1.5 HotFixes to March 2009)
Custom Columns updated in the Results Table
When Custom Columns were added in the acquisition Batch Editor, only the first compound was
updated in the Results Table after quantitation. The remaining compounds displayed N/A. This
Analyst® 1.6.2 Software
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Release Notes
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Enhancements and Fixes
issue has been fixed. All compounds are updated in the Custom Columns. (SCR 15535)
(Analyst® 1.5 HotFixes to March 2009)
Quantitation of Scheduled MRM algorithm data file
An internal change has been made to the way in which Analyst® software handles data layouts in
the Results Table. Now the summary columns are handled in a more consistent fashion. This
change is transparent and will have no functional impact to this feature. (ST 8250) (Analyst® 1.5
HotFixes to March 2009)
Expected RT and RT Window values no longer set to zero in the Results Table
When a Results Table was created and a peak was not found for a particular sample, the
associated Expected RT and RT Window values were set to zero in the Results Table. Changing
the integration parameters to correctly integrate these peaks would populate the correct
Expected RT and RT Window values. This issue has been fixed. The Expected RT and RT
Window values are now populated whether or not a peak is found. (TT 5447) (Analyst® 1.5
HotFixes to March 2009)
Other
4000 QTRAP instrument compatible with DuoSpray and PhotoSpray ion sources
With the previous Configuration Table, the 4000 QTRAP instrument (AR series) did not recognize
the DuoSpray and PhotoSpray ion sources. An updated Configuration Table has been included in
this release. To fix this issue, update the Configuration Table (B9609031.FW) on the 4000
QTRAP instrument. (SCR 15548) (Analyst® 1.5 HotFixes to March 2009)
Resolution settings saved after copying
When you copy experiments in the acquisition method, the resolution settings were not saved.
Re-enter this information. This issue is now fixed. (SCR 13080)
New Enhancements and Fixes in the Analyst 1.5
Components for 5500 Systems
With the exception of the last item in this section, the following information describes support for
the AB SCIEX QTRAP 5500 System and the AB SCIEX Triple Quad 5500 System.
.
Note: For reference, the name of the software patch or HotFixes release where the
issue was previously fixed is included.
Acquire — Acquisition and Batch Editor
Faster Linear Ion Trap (LIT) scan rates
The system performs LIT scans in all modes at up to 20000 Da/s, as well as 1000 and 10000 Da/
s. In addition, Enhanced Resolution scan types are available at 50 and 250 Da/s.
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
41 of 100
Enhancements and Fixes
Pre-set quadrupole scan rates
Quadrupole scanning is now done at fixed scan rates (up to 2000 Da/s), which simplifies
operation for the customer while ensuring good data quality.
Better Quadrupole and LIT sensitivity relative to the 4000 QTRAP system:
•
Better quadrupole sensitivity means increased MRM sensitivity resulting in lower
limits of quantitation.
•
Better LIT sensitivity means better qualitative and quantitative data.
Faster polarity switching
The system is capable of switching polarity in only 50 ms, which is more than 10 times faster than
our existing systems.
Quadrupole MRM improvements
Shorter transit times across the improved LINAC® collision cell allow lower dwell and pause
times to be used for multiple MRM experiments. Up to 1250 MRM transitions are now supported
in a single experiment, and up to 2500 MRM transitions using the Scheduled MRM algorithm.
Quadrupole scanning improvements
The improved LINAC collision cell also leads to better precursor and neutral loss scanning, with
scan rates up to 2000 Da/s at unit resolution.
Other
Communication via Ethernet now available
The communication between the system and the acquisition computer is now provided through
an Ethernet connection instead of a GPIB connection.
Integrated syringe pump and integrated diverter valve available
The system is equipped with an integrated syringe pump and integrated diverter valve. You can
start these devices manually or control them through the Analyst software.
Notes on Use
•
In the DFT Method Options, the target TIC values are optimized for the 10000 Da/s
scan speed with the exception of the Enhanced Resolution target TIC, which is
optimized for the 250 Da/s scan speed. These values are suitable for all other scan
speeds.
•
By design, if the integrated syringe pump is configured in a method, the syringe
pump will remain running after completing a run until the Max Idle Time is reached.
You must manually stop the syringe pump after you have completed Instrument
Optimization if you want to stop the flow from the syringe pump. Instrument
Optimization will not turn off the syringe pump.
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Release Notes
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Enhancements and Fixes
Tip! You can adjust the Max Idle Time in the Queue Options by clicking
Tools > Settings > Queue Options.
•
The Analyst software operation may be slow in the areas of the Method Editor,
Explore, and Quantitation when dealing with a large number of MRM transitions.
•
Make sure that you have a printer configured before running Instrument
Optimization.
•
The Queue must be in Ready state before you start the syringe pump: If the Queue
is in Standby mode, put the queue in Ready state before starting the syringe pump.
IntelliQuan parameters now selected in peak list tab for data acquired using the
Scheduled MRM algorithm
When data acquired using the Scheduled MRM algorithm are opened, the corresponding peak
list will now correspond to the recommended integration algorithm. Previously the Analyst
Classic algorithm was being applied instead of the IntelliQuan algorithm to data when the first
sample in the data file was not a Scheduled MRM sample. (ST 6981)
New Enhancements and Fixes in the Analyst 1.5
Software and the Analyst 1.4.2 HotFixes
.
Note: For reference, the name of the software patch or HotFixes release where the
issue was previously fixed is included.
Audit Trail
Actions logged to the correct Audit Trail*
It has been noted that if a user changes the active Project while data is being acquired, the Audit
Trail will show data being added to the newly selected project rather than the original one. This
issue has been resolved, and now changing the active project while data is being acquired will
not affect which Audit Trail information is logged to. (SCR 15270) (Analyst® 1.4.2 HotFixes to
July 2007)
*These actions require that the Audit Trail is set to record the described actions
Record Modified flag now clears
If a user manually integrated a sample and accepted the changes but then manually cleared the
“Manual Integration” check box and accepted that change, the Results Table reverted to the
original (automatic) integration, but the Record Modified flag still remained. This has been
corrected and now manually clearing the “Manual Integration” box and accepting the changes
clears the Record Modified flag. (SCR 15161) (Analyst® 1.4.2 HotFixes to July 2007)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
43 of 100
Enhancements and Fixes
Canceling a manual integration no longer flags a sample as modified
When e-Signatures were required as per the Audit Trail settings, and if a user manually
integrated a sample but clicked “Cancel” when prompted for an e-signature, the sample reverted
to its original (automatic) integration, but the Record Modified flag remained. This has been
corrected and now clicking Cancel when prompted for an e-signature now clears the Record
Modified flag. (SCR 15338) (Analyst® 1.4.2 HotFixes to July 2007)
Updating the method now clears the check box
If a user manually changed a method parameter on a sample and accepted the change, then
right-clicked on the chromatogram and selected “Update the Method” the user was asked if he/
she would like to update all peaks, as opposed to only those which have not been manually
integrated. If the user selected “No” (Update only those not manually integrated), the Record
Modified flag was cleared for all manually integrated samples but the Manual Integration box
remained checked on the chromatogram. Analyst® 1.4.2 HotFixes to July 2007 corrects this
issue and the Record Modified flag remains checked for all manually integrated samples. (SCR
15160) (Analyst® 1.4.2 HotFixes to July 2007)
Record Modified flag now accurately reflects the modification status of the sample
Incorrect behavior of the record modified flag was found in the following scenarios:
•
The Record Modified flag for a manually integrated Analyte Peak is set to “off” when
the integration parameters for its Internal Standard peak are modified and globally
updated.
•
The Record Modified flag remains checked “on” for some Analyte peaks even after
the integration method for all samples is reset using the “Update Method” operation.
This behavior has been corrected and the record modified flag is now set properly for these
scenarios. (SCR 15506) (Analyst® 1.4.2 HotFixes to May 2008)
Audit Trail archives correctly
For quantitation Results Tables, this issue cannot occur. However, for project and instrument
audit trails, in rare cases where the audit trail exceeded 1000 records (for instance, when there
are a large number of subprojects), and the user has been denied “modify” permissions for the
audit trail folder, a situation could have occurred where these audit trails became unpopulated of
archive events.
The audit trails for the project and instrument automatically archive after 1000 records are
written. The audit trail is saved in the Project Information folder with a name indicating the type of
audit trail and the date and time. A new audit trail is then created with the first record giving the
path of the previously archived audit trail.
In the Analyst software version 1.4.2 and earlier, if the user both did not have Windows “modify”
permissions and was not explicitly given “delete” permissions, an empty archive file was created
that did not show the audit trail records. With this release, neither “modify” nor “delete” rights are
required to successfully archive audit trail files. However, Windows read and write access is still
required. (SCR 15516) (Analyst® 1.4.2 HotFixes to May 2008)
Analyst® 1.6.2 Software
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Release Notes
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Enhancements and Fixes
Acquire — Acquisition and Batch Editor
Scheduled MRM™ algorithm now available
Scheduled MRM algorithm provides the ability to monitor up to a thousand potential analytes in a
single chromatographic run. This can be accomplished by supplying a list of MRM transitions and
their corresponding retention times and compound IDs, a time window, and a target or desired
cycle time such that the system can automatically acquire only the necessary MRM transitions at
any given time during a run. On QTRAP instruments, this method can service screening
applications with triple quadrupole MRM selectivity and LIT MS/MS simultaneously by focusing
on only a few analytes at a time, allowing extra time for MS/MS scans.
The Scheduled MRM algorithm functionality can also be used in an Information Dependent
Acquisition (IDA) experiment to maximize screening and confirmation capabilities.
DBS (Dynamic Background Subtraction™) functionality now fully integrated
DBS functionality improves the ability of the mass spectrometer to find more analytes in a
chromatographic run while using IDA. By subtracting predicted analyte signal from the analyte(s)
of focus during the course of an IDA run, DBS dynamically filters new analytes from the
background noise. This functionality is now fully integrated into the software as a check box on
the First Level Criteria tab of an IDA experiment.
Methods for Agilent 1100 devices are compatible with Agilent 1200 devices
Methods created with an Agilent 1100 stack will now open or run when a functionally equivalent
Agilent 1200 stack is configured. For example, if the 1100 method contained an isocratic pump
and wellplate autosampler, this method did not open or run when connected to a 1200 isocratic
pump and 1200 wellplate autosampler. Upon installation of this release, users who have created
methods on their Agilent 1100 stack are able to use them on a functionally equivalent Agilent
1200 stack without having to recreate the methods. [Please note that the Agilent 1200 highpressure devices (G1312 B pump, G1367C autosampler, G1316 C column oven) are not
considered functionally equivalent to any Agilent 1100 device. Therefore, a user will still not be
able to use their 1100 methods when a 1200 high-pressure device is configured.] (SCR 15141)
(Analyst® 1.4.2 HotFixes to November 2006)
Note: The information for Agilent 1100 devices which is available in the Help is also
valid for Agilent 1200 devices.
Delay times now properly applied
When a method was created with a delay time greater than 30 seconds and was run in a batch,
the delay times were occasionally longer or shorter than what was specified. This issue has been
resolved. Acquisition Delay Times now reflect the times specified in the method. (SCR 15142)
(Analyst® 1.4.2 HotFixes to November 2006)
Improved data capacity
To accommodate the larger data size introduced by the Scheduled MRM algorithm functionality,
.wiff data file compression has been introduced. As a result, the data capacity of files is now
improved.
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
Dynamic Fill Time (DFT) improvements
Improvements have been made to the DFT to better control the number of ions in the linear ion
trap. This can result in improved spectral quality.
QTRAP data available for EPI scans in IDA methods
In a small number of cases, an issue was observed on the QTRAP series of instruments
involving Enhanced Product Ion (EPI) scans in IDA methods occasionally failing to fragment the
parent ion. Analyst® 1.4.2 HotFixes to July 2007 resolves this issue and EPI scans in IDA
methods will collect data properly. (SCR 15360, SCR 15298) (Analyst® 1.4.2 HotFixes to July
2007)
Tune and Calibrate
Tune enhancements
A fully automated Instrument Optimization tuning function, formerly offered as a script called
“AutoTune” has been fully integrated into the Analyst 1.5 or later software. The instrument
optimization feature automatically tunes your instrument for you in minutes, saving time and
effort formerly used in the mass calibration process. Because Instrument Optimization includes
the optimization of the resolution of the instrument, Resolution Optimization has been removed
from the Tune and Calibrate module. In addition, Quantitative Optimization has been renamed
Compound Optimization and the Tune mode as a whole has been renamed Tune and Calibrate.
Explore
XIC no longer shows empty graphs
In rare cases, selecting the XIC in Explorer could result in an empty graph. The HotFix corrects
this issue, and the XIC shows the appropriate data. (SCR 15198) (Analyst® 1.4.2 HotFixes to
November 2006)
Quantitate
Several updates have been made to the peak integration in the Analyst 1.5 software. These
updates have been made with the following principles in mind:
•
Updates apply to the IntelliQuan peak integration mode; that is, the IQA and MQII
algorithms. The Analyst Classic peak integration mode remains unaffected.
•
The updates are well-documented in the software; quantitative results that use the
updated algorithms are labeled IQA II and MQ III in the Results Table.
•
Previous Results Tables (created in versions of the Analyst software earlier than
version1.5) will continue to use the non-updated peak integration in the Analyst 1.5
and later software (as opposed to the updated IQA II and MQ III). This is true even if
such Results Tables are opened with the Analyst 1.5 and later software, modified
and re-saved. To use the new algorithms, create a new Results Table from scratch.
•
All new Results Tables in IntelliQuan peak integration mode are created using the
updated IQA II and MQ III algorithms.
Analyst® 1.6.2 Software
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Release Notes
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Enhancements and Fixes
A full technical explanation of the changes is included in Technical Information Regarding
Integration on page 99.
For faster review of peaks in Quantitation mode, a measure has been added to indicate the
quality of integration of peaks. This new feature is available through the addition of two new
columns in the Results Table named “Analyst Integration Quality” and “IS Integration Quality”.
Values closer to 1 indicate well-integrated peaks and values closer to 0 indicate that the peak is
not well-integrated. This indicator makes reviewing manual peaks easier because operators can
focus on the lower values to guide manual review of substandard peaks.
Quantitation Optimization above mass 998 is successful
When the Quantitation Optimization wizard was run on an API 5000 instrument (or in API 5000
system simulation mode) with a mass above 998 resulted in the message: “Quantitation
Optimization Failed”, followed by an “Unspecified Error” window. This issue is now fixed and
optimization proceeds correctly. (SCR 14889) (Analyst® 1.4.2 HotFixes to November 2006)
Results Table Saving action logged in audit trail during QA Review*
When a user assigned the QA Reviewer role opened a Results Table and then attempted to
close it, they were prompted “Do you want to add an annotation about your QA Review to the
audit trail for this results table? Yes / No / Cancel”. Even if the user selected “No” they were
prompted for an e-signature and a saving action was logged in the Audit Trail. With this release,
there is no prompt for an e-signature, and no saving action is logged unless an annotation is
added. (SCR 14911) (Analyst® 1.4.2 HotFixes to November 2006)
Results Tables deleted on overwrite now logged in the Audit Trail*
With a Results Table active, a user could click File > Save As, and choose to overwrite an
existing table. If the auditing capabilities were enabled, the user was prompted to input a reason
for this action. Selecting “Cancel” at this point resulted in the deletion of the existing Results
Table. No action was logged in the Audit Trail. After installing this release, the existing Results
Table is neither deleted nor modified in the case described above. (SCR 15081) (Analyst® 1.4.2
HotFixes to November 2006)
*These actions require that the Audit Trail is set to record the described actions.
Discrepancy Between Results Table and Chromatogram is now corrected
If a user built a Results Table based on samples that were still being acquired, the Analyst
software built the Results Table based on the information available at the time. This could lead to
the Results Table showing results that did not agree with the associated chromatograms as
shown in the Peak Review window. The Analyst software did not automatically update the
Results Table after acquisition is complete.
Following installation of this release, when a user runs the Quantitation Wizard, samples which
are in the process of being acquired will not be displayed in the wizard. This prevents users from
selecting them and potentially generating incorrect results. If a user runs the Quantitation Wizard
during acquisition, he/she will need to build a new Results Table or manually add the samples to
the Results Table after the acquisition has completed in order to include samples which were not
added because they were still being acquired at the time of the table’s creation. (SCR 12842)
(Analyst® 1.4.2 HotFixes to July 2007)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Enhancements and Fixes
Area discrepancy between the Results Table and peak review is now fixed
In the Quantitation module, in rare cases, small discrepancies were reported between the
Results Table peak area and the peak review peak area. In sites that reported experiencing the
issue, fewer than 1 in 2000 integrations were affected. The issue has been addressed. See
Technical Information Regarding Integration on page 99. (SCR 15517) (Analyst® 1.4.2 HotFixes
to May 2008)
Smoothing Value on reports is now printed
When a Quantitation report was printed for a manually integrated report, the smoothing value
used was not printed on the report. This has been corrected and the smoothing value used is
now shown. (SCR 14974) (Analyst® 1.4.2 HotFixes to July 2007)
Quantitation Parameters prints correctly when using IntelliQuan
When printing a Quantitation report for which the Integration Algorithm was set to IntelliQuan, the
Integration Parameters shown on the report was actually the settings for the Analyst Classic
Algorithm. This issue is fixed and now IntelliQuan reports will properly show the integration
parameters used. (SCR 14340) (Analyst® 1.4.2 HotFixes to July 2007)
Peripheral Devices
The Analyst 1.5 software provides additional support for the following:
•
Autosampler layout database for the Spark Holland Alias autosampler controlled
through the Analyst Access Object (AAO) interface. (SCR 15523)
•
Autosampler layout database for the Agilent autosampler AS G1367C Hip-ALS SL.
•
Agilent DAD 1315D. (ST 17089)
Support for the following Shimadzu LC-20A Prominence devices:
•
Controllers: CBM-20A
•
CBM-20A Lite
•
Pumps: LC-20AT
•
LC-20AD
•
LC-20AB
•
Detectors: SPD-20A
•
SPD-20AV
•
RID-10A
•
RF-10A
•
RF-10Axl
•
AutoSamplers: SIL-20A
•
SIL-20AC
•
Rack Charger
•
Ovens: CTO-20A
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Release Notes
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Enhancements and Fixes
•
CTO-20AC
(SCR 14795, SCR 15282) (Analyst® 1.4.2 HotFixes to November 2006)
Support for Agilent 1200 DAD is now included
Support for the Agilent 1200 G1315 D Diode Array Detector. (SCR 15296) (Analyst® 1.4.2 Patch
for Agilent 1200 G1315 D DAD)
Shimadzu FIA Quantitation Optimization Isocratic Method now recognized
Following the installation of Analyst® 1.4.2 HotFixes to July 2007, attempting to perform FIA
Quantitative Optimization with Shimadzu devices configured natively within the Analyst software
caused a message to appear informing the user that an isocratic method was needed. This
occurred even when an isocratic method was provided. This issue is resolved and users can
once again use Shimadzu devices to perform FIA Quantitative Optimization. (SCR 15516)
(Analyst® 1.4.2 HotFixes to May 2008)
Other
Displaying File Information may have caused Analyst software to stop responding
In a rare number of instances, displaying the File Information for certain files caused the Analyst
software to stop responding. This issue has been fixed. (SCR 15195) (Analyst® 1.4.2 HotFixes to
November 2006)
The list of devices contained in an Analyst method is now returned
Program level access to Analyst method components (through use of the Analyst software SDK)
would not return the list of devices contained in the Analyst software method. This issue is fixed
and the full list of devices in a method is returned. (SCR 15240) (Analyst® 1.4.2 HotFixes to
November 2006)
AAO batch acquisition error
LC and other peripheral device vendors (excluding Agilent, Shimadzu, and CTC) use the Analyst
Acquisition Object (AAO) interface to run their device drivers. When running long batches with a
driver using the AAO, the batches intermittently fail. This issue has been fixed. (SCR 14842)
(AAO Development Kit for Analyst® 1.4.2 HotFixes to November 2006)
Calling ConfigureBatch() in AAO with more than one template mass range caused
issue with column names
When using the AAO, the ConfigureBatch() command would result in erroneous column names
being used if more than one template mass range was specified. This has been corrected with
this release and calling ConfigureBatch() with more than one template mass range now results in
the proper column names being created. (SCR 15187) (AAO Development Kit for Analyst® 1.4.2
HotFixes to November 2006)
Quantitation method reference included in .wiff files acquired by submitting batch
through AAO
When submitting a batch through the Analyst software, a reference to the Quantitation Method
used in the batch is created in the .wiff file. However, when submitting a batch via AAO, the
Release Notes
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Enhancements and Fixes
reference to the Quantitation method was missing from the resulting .wiff file. This error has been
corrected in the HotFixes to November 2006, and now batches submitted via AAO which contain
a reference to a Quantitation Method will have the Quantitation Method included in the resulting
.wiff file. (SCR 15169) (AAO Development Kit for Analyst® 1.4.2 HotFixes to November 2006)
Added AAO event to notify client of change in the Analyst software project
When a new active project is selected within Analyst software, a new ProjectChange event
containing the name of the newly selected project is fired from AAO, allowing the client
application to be programmatically synchronized. (SCR 12965) (AAO Development Kit for
Analyst® 1.4.2 HotFixes to November 2006)
Added AAO event to notify client of changes to Analyst software method file
In the Analyst software, on saving of a method file containing the AAO client application method,
a new MethodRequested event is fired from AAO to notify the application of the save. The client
application can then respond by calling a new method IAAO_Method::SendXMLMethodData()
with the latest XML method data corresponding to the Analyst software method, which will then
be passed back into the Analyst software and then saved into the method file, ensuring the
methods in the Analyst software and in the client application are synchronized. (SCR 12963)
(AAO Development Kit for Analyst® 1.4.2 HotFixes to November 2006)
Added ability to store Analog Detector information to Analyst software data file
DAD (Diode Array Detector) and ADC (Analog-to-Digital Converter) data acquired from
peripheral devices controlled by AAO client applications can now be stored in real-time into the
Analyst software .wiff data file via interface methods in IAAO_Acquire. (SCR 12958) (AAO
Development Kit for Analyst® 1.4.2 HotFixes to November 2006)
Support for ADC Card PCI-6289 and NI-DAQmx 8.3
The Analyst software now supports the National Instruments PCI- 6289 ADC card as well as NIDAQmx driver version 8.3. The new driver is required for the new ADC card, but also supports
the existing model PCI-6032E. Therefore, this driver change will be transparent to the user, and
will not affect any existing functionality. (SCR 15442) (Analyst® 1.4.2 HotFixes to July 2007)
Note: The existing driver for the ADC Card must be replaced if this release is installed
on a PC where an ADC Card is currently installed.
Quantitation Optimization for AAO applications
Previously, Quantitative Optimization (Infusion) could not be performed with AAO-controlled
devices, as the mass spectrometer would wait indefinitely for an injection to take place. This has
been resolved and the mass spectrometer will no longer wait for an injection as methods are now
configured in the NO SYNC mode. As a result, Quantitative Optimization will proceed as
expected. (SCR 14921) (Analyst® 1.4.2 HotFixes to July 2007)
FIA Quantitation Optimization for AAO applications
When performing Quantitative Optimization with FIA, the wizard checks the method for an
isocratic LC pump method and if an autosampler is present, will set up the display for the user to
pick the rack, sample position, and so forth. With Software Applications using the AAO, this did
not work and the wizard thought the method is a mass spectrometer-only method. This is now
fixed and support for external AAO applications is implemented. AutoSamplers controlled via
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AAO can now be configured (including rack/plate/vial selection) during the FIA Quantitative
Optimization wizard. (SCR 12956) (Analyst® 1.4.2 HotFixes to July 2007)
Manual Tune now works with AAO controlled devices
Previously, during manual tune the user was not allowed to build methods for devices controlled
by the AAO. This has been corrected and LC Pumps controlled via AAO can now be used to
build a method as part of the Analyst software manual tune operation. (SCR 12977) (Analyst®
1.4.2 HotFixes to July 2007)
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Notes on Use, Known Issues, and Limitations
The following is a list of known issues, limitations, and important notes on using the software.
There may be other issues or limitations with the Analyst® 1.6.2 software in addition to those
listed below. If you find additional issues, email support@absciex.com.
In general, if the Analyst software is not responding, restarting the software may help. If this does
not work, restart the computer to make sure the Analyst Service software and device drivers
restart.
Guidance for Antivirus and Backup Software
While it is a widely acknowledged good practice to employ antivirus and backup software, these
applications may interfere with the real-time nature of the Analyst software. Some antivirus and
backup applications are configured by default to automatically scan and archive a file
immediately after creation. Because the Analyst software can perform multiple writes to a single
data file during an acquisition sequence, it is important to disable these real-time features to
prevent the antivirus or backup software from locking the data file while it is still needed by the
Analyst software application. Many widely-used applications can be configured to either disable
real-time protection, or ignore certain file-types (for example, .rdb, .wiff and .wiff.scan files).
Failure to do so may result in either failed acquisitions or acquisitions that take longer to
complete than expected.
In general, the antivirus or backup software on the Analyst software acquisition workstations
should be configured in a manner that will disable real-time scanning and archiving of files in the
Analyst Data folder. For example, when configuring the Symantec Endpoint software, the
following settings have been found to increase performance during data acquisition:
•
Antivirus and Antispyware Protection > File System Auto-Protect > File Types:
Choose “Selected” and then make sure that the Extensions list does not contain
.wiff, .wiff.scan, or .rdb file extensions.
•
Antivirus and Antispyware Protection > File System Auto-Protect > File Types >
Advanced > Scan files when: Scan when a file is modified.
For instructions on how to best configure your particular antivirus or backup software, contact
your antivirus or backup software provider.
Guidance on File Encryption
When using software to encrypt the contents of your hard drive, make sure that the Analyst Data
folder is not encrypted. Failure to do so may result in failed acquisitions or corrupted data files.
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Audit Trail
Analyst software use in an RDP (Remote Desktop Protocol) Environment (that is
Citrix)
We do not recommend that you access the Analyst software using RDP. Users who access the
Analyst software using RDP are logged in the Analyst software audit trail. Any subsequent users
who log in to the Analyst software at a workstation that is running RDP will be recorded in the
audit trail using the credentials of the first user.
Special characters fix
Although audit trail entries occurring after the installation of the Analyst 1.5 software appear
properly, this release does not address those entries made by prior versions of the Analyst
software. In some instances, records containing certain special characters not used in the
English language (for example, é, ö) are not visible in the audit trail; however, they can still be
retrieved by searching or filtering the audit trail by date. (ST 14394)
Some specific special characters will not appear properly even following the installation of the
Analyst 1.5.1 software. Audit trail records will display correctly, but these special characters will
appear differently in the record. (ST 14394)
For example:
Д will appear as a box
Ň will appear as a G
ß will appear as a superscript z
Avoid using the above characters in the audit trail.
Wrong audit trail information with manual integration
The information in the audit trail is incorrect when you choose to revert back to the manual
integration results (that is, when Reject Manual Integration is set). It shows Change Reason and
E-signature even though they are not set to prompt for input. (SCR 13761)
Audit event deselected unexpectedly
In the Audit Map Editor dialog, if you right-click the Audited column and click Fill Down, the
Project Settings Have Been Changed and Instrument Settings Have Been Changed Events
check boxes may be deselected. Do not use Fill Down over these events. (SCR 14266)
Closing the IDA file is not logged as event in the audit trail
If you close an IDA data file, the event is not logged in the audit trail. (ST 9487)
The Analyst software stops responding when performing print preview
When you select to print preview an audit trail that has more than 100 records using the All
Pages menu option (right-click), the Analyst software may stop responding. You can preview one
page at a time using the Current Page menu option instead. (ST 4284)
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Audit trail printout columns truncated
When printing the audit trail in both Portrait and Landscape modes, some columns may be
truncated. In some cases, this issue may be minimized by printing in Landscape mode.
(ST 2261)
Wrong module recorded in audit trail
When you change a Quantitation algorithm to another algorithm, the audit trail incorrectly records
the module name as “Build Acquisition Method”. (ST 4922)
Error when printing a large audit trail
Printing the audit trail from the active Results Table (Tools > Audit Trail > Show) may cause an
error if there are more entries in the audit trail than can be printed on a single page. Print audit
trails only from within the Audit Trail Manager (Menu Bar: View > Audit Trail Manager). (ST 6374)
Audit events on network server
When writing audit events to a project residing on a network file server, the audit information will
use the network server clock time instead of the local computer time. This is expected behavior.
(SCR 12390)
Configure — Administration/Security
Usernames should not contain spaces
While Windows supports the use of usernames containing spaces, the Analyst software does
not. If in Mixed Mode security, a user attempts to log into the software with a username
containing a space, the Analyst software will display an error and fail the login. (AN-50)
Managing Windows operating system file permissions
To use the Analyst software to manage Windows operating system file permissions, give the
Analyst software Administrator software change permission rights for the project folders. This
includes any network-based project folders.
Stopping the AnalystService
Only local administrator group members are allowed to stop the AnalystService (the Acquisition
part of the Analyst software). If other users need to stop the service, see the Microsoft
Management Console for configuration instructions. Alternatively, users can restart the computer.
Method editor access
You must have read and write permissions for the Project Information folder to access the
method editor. If you have read-only permission and try to open the method editor, the system
may stop responding. (SCR 8037)
Mapped network drives might not be visible in Mixed Mode
When setting the Root Directory in the Analyst software Mixed Mode security environment, the
Browse for Folder dialog does not always show the mapped network drives. Use the computer
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Notes on Use, Known Issues, and Limitations
name in the UNC (Universal Naming Convention) format (\\computer name\drive name) instead
of the mapped letter. (SCR 11094)
The Analyst software does not start if you have no file permissions
You cannot start the Analyst software if the root directory is set to a network drive for which you
have no file permissions set. If the person trying to log on is an Administrator, the Analyst
software prompts for an alternate root directory. (ST 9836)
Screen lock wait time incorrect in the audit trail
In the audit trail data, the wait time recorded for the Screen Lock in the Security Configuration is
incorrect. There is also no audit record created when the Wait time for the Screen Lock and Auto
Logout fields are modified. (SCR 12935)
Issue deleting user-defined role
Before deleting a user-defined role, remove all users assigned to this role. If you do not remove
users, the results may not appear properly.
Unlocking the Analyst software using the UPN name format
When attempting to unlock the Analyst software using the UPN format and a user (with unlocking
rights) who was not logged into the software when it was locked, the Analyst software displays an
error stating that the user is not recognized. This happens whether or not the new user is a
legitimate user on the domain. To unlock the software, click OK on the error window and type the
new user’s credentials a second time (in UPN format).
Disabling access to “Select processing algorithm” does not take effect
Although access to the “Select processing algorithm to retrieve peak list” for Explore function is
disabled for a user role, the user with this role can still modify the integration algorithm for
retrieving the peak list.
Help Find
To activate the Find tab in the Help for the first time after installation, you need to be the Windows
local administrator or have the equivalent rights. Otherwise, the message Unable to display the
Find tab (177) appears. (SCR 13792)
Screen lock settings not retained on install
After the Analyst software is installed, the Network Acquisition account screen lock settings are
not retained. Re-type this information in the Security tab of the Security Configuration dialog.
Configure — Hardware Configuration
Possible issue activating Shimadzu hardware containing Nexera devices when
upgrading from a previous version of the Analyst software
In some rare cases, after upgrading to the Analyst 1.6.2 software from a previous version, users
might be unable to activate a hardware profile containing Shimadzu Nexera devices. However, if
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the user edits the hardware profile and sets the P.Max setting to Auto or Off, the profile activates
properly. (AN-46)
Incorrect profile shown in the error message
The hardware profile dialog may show an incorrect profile in the error message when failing to
activate a profile. (SCR 13820)
Incorrect DuoSpray™ Ion Source Switching Valve Counter value
During IDA acquisition, the value in the DuoSpray™ Ion Source Switching Valve Counter field in
the hardware profile is incorrect. (SCR 13635)
Temperature Reached may intermittently show while the Turbo V™ ion source is
cooling
If the Turbo V ion source temperature is set to a value lower than the current setting, the ion
source may intermittently report “Temperature Reached” while it is cooling. Users should allow
the system to cool or stabilize for the recommended time while the source is cooling. (TT 35398)
Deactivate hardware profile error message appearing during uninstall
Occasionally, when uninstalling the Analyst software, a message asking the user to deactivate
the hardware profile appears even if the hardware profile has been deactivated. To clear this
issue, restart the Analyst software. (ST 16060)
Configure — Acquisition Method Editor
Method Editor user interface (UI) issue when modifying scan type and polarity of a
saved method
If the user opens a previously saved MRM method and then changes both the scan type and
polarity without switching tabs between changes, an error is shown and the method tabs
(Source, Compound, Resolution) are empty. If users are working with saved methods, they
should change tabs when making changes scan type or polarity, to refresh the method UI.
(AN-48)
Filename is lost from the UI when resaving an existing method that fails validation
If after the user opens (or creates and saves) a method, modifies the method, and then tries to
resave, the method fails validation and an error is shown. The filename is no longer shown in the
top of the Analyst software window, and the user is prompted to select a new filename if they try
to save once again. (AN-78)
Different CEM values for multi-experiment methods with polarity switching is not
supported
When creating multi-experiment methods, users can choose to switch polarities between
experiments. If this option is selected, users should not choose different CEM values for the
experiments. If they do, the CEM values are not applied correctly during acquisition. Users
should set the same CEM value for all experiments when using polarity switching. (CBUFW-25)
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Ionspray (IS) values should be the same for all experiments in the same polarity
When creating a multi-experiment method with a single polarity, users should set the Ionspray
(IS) voltage to the same value for all experiments. If users select differing IS voltages, the
voltages are not applied correctly during acquisition. (CBUFW-25)
Tune and Calibrate — Compound Optimization
Transitions with the same name may not optimize correctly during Compound
Optimization
When using the automatic Compound Optimization option, use a different name for each
transition to be optimized. If the same name is selected for more than one transition, some
parameters will not optimize correctly for the duplicate transition. (SCR 9450)
Use of Shimadzu and Tempo MDLC devices when performing infusion Compound
Optimization
The software will not optimize if the Shimadzu and Tempo™ MDLC devices are included in the
hardware profile. Remove them from the hardware profile before performing this operation or
create a second hardware profile that includes only the mass spectrometer that you can use for
infusion Compound Optimization.
The Compound Optimization report shows that DP is ramped between 0 and 400
Volts
On the 5500 series of instruments, the actual range for the DP ramp used during the optimization
is 0 and 300 Volts. (ST 9248)
Compound Optimization does not start the integrated syringe pump for an
API 3200™ system
Users can either start the syringe pump using Manual Tuning or they can use an external syringe
pump. (ST 11130)
Tune and Calibrate — Instrument Optimization
Unable to switch to Tune mode
After performing Instrument Optimization, the Analyst software may not be able to switch to Tune
mode. The Tune button on the toolbar may be disabled. If this occurs, deactivate and then
reactivate the hardware profile again and then switch to Tune mode. (ST 7002)
Empty subfolders in Instrument Optimization folder
Empty subfolders are created in Analyst Data\Projects\API Instrument\Data\Instrument
Optimization if Instrument Optimization is cancelled on the final page of the wizard (instead of
clicking GO!). (ST 3767)
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Additional 1 Da on Results Graph
When viewing the results summary, the graph shows an additional 1 Da on either side of the xaxis. This does not affect the accuracy of the graph. (ST 3775)
Click More Options to see More Tuning Options
When in the Select the scan mode screen, clicking More Options allows you to set additional
Instrument Optimization parameters. This does not pause the Instrument Optimization wizard
and the wizard can continue while this screen is open. (ST 3763)
Instrument Optimization stops responding when the Start Over button is pressed
Occasionally Analyst software stops responding if you press the Start Over button after you have
run Instrument Optimization several consecutive times. Restart Instrument Optimization from the
Analyst Navigation bar instead of using the Start Over button. (ST 8029)
On rare occasions, the Queue Manager is inaccessible after running Instrument
Optimization
To correct this issue, deactivate the hardware profile, restart the Analyst software, and then
activate the hardware profile. (ST 9678)
Instrument Optimization fails to run after installation
Occasionally, after removing and reinstalling the Analyst software, Instrument Optimization fails
to run and returns the error, “The current hardware profile is not supported by Instrument
Optimization.” To run Instrument Optimization, remove the Analyst software and then reinstall.
Correct masses are occasionally not selected when using the Alternate Tuning
option
If you are using Instrument Optimization to tune a system, it is highly recommended that you use
the approved tuning solution. If you use an unapproved solution, some masses may not be
correctly calibrated.
Occasionally, calibration shifts are observed after optimization of the 12 000 Da/s
scan speed on the 5500 series of instruments using Instrument Optimization
If this occurs after Instrument Optimization, you can restart the optimization process, or manually
calibrate the masses that are out of calibration.
Occasionally, Instrument Optimization becomes unresponsive during tuning
If this happens, do not close or restart the Analyst software. Use the Task Manager program to
close Instrument Optimization and then restart Instrument Optimization. (ST 13044)
Typing a negative value for the IonSpray source voltage in Negative mode causes
the optimization to fail
When running Instrument Optimization in Negative mode, type IonSpray™ source voltages as
absolute (positive) values. (ST 3778)
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Poor data quality during instrument optimization tuning
Occasionally, the Analyst software will scan less than the number of MCA scans selected in an
acquisition method. For example, the software will only return 3 scans for a Q1 scan when 10
MCA scans are specified. This MCA issue may affect Instrument Optimization. If this occurs
during Instrument Optimization, restart the optimization process. (ST 13460)
Tune and Calibrate — Manual Tuning
Application Event Log errors generated while operating QTRAP® 4500 LC/MS/MS
system in Manual Tune
When the QTRAP 4500 LC/MS/MS system is operated in the Manual Tuning mode, the Windows
Application Event Log shows the following error: "DDMSMassSpec, Process.cpp, Line 2399,
EF:0x20000016=Unknown word <DPF> read". This error can be ignored and it has no affect on
system operation. (AN-265)
GS2 is available when the APCI probe is in use (specific to the 3200 series of
instruments)
When the APCI probe is installed, the GS2 parameter is available, but should not be. When using
the APCI probe, set and leave the GS2 value at 0. (SCR 14506)
Display of metrics for mass calibration
Metrics for mass calibration do not show all the masses used if the calibration peak list is not in
numerical order. (SCR 8483)
Instability in Manual Tune
If the Graph Information pane is open in Manual Tune, the system may stop responding if one
run is terminated and a new one started. Closing the Graph Information pane may prevent this.
(SCR 8879)
Possibility of incorrect TIC data when ramping parameters using negative step
size
Ramp parameters with a positive step size only. Negative step sizes, may yield incorrect TIC
data.
Offset drop from unit resolution for the API 3200 instrument
For the API 3200™ instrument, when tuning, set the correct Offset Drop from Unit Resolution
values in the Tuning Options Resolution tab.
•
In the Low Resolution group, in the Offset Drop from Unit Resolution box, type 0.03.
•
In the Open Resolution group, in the Offset Drop from Unit Resolution box, type 0.5.
Syringe diameter does not change during acquisition
On the 5500 series of instruments, if you change both the syringe pump diameter and flow rate
while the syringe pump is running and then click Set Flow Rate, the flow rate changes but the
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diameter does not. You must stop the pump and then restart it for the changes to be applied. (ST
8291)
Data is not being recorded for the same number of cycles as requested when MCA
is selected
Occasionally, the Analyst software will scan less than the number of MCA scans selected in an
acquisition method. For example, the software will only return 3 scans for a Q1 scan when 10
MCA scans are specified. To correct this issue, restart the scan or toggle between scan speeds
and then restart the scan. (ST 13460)
Windows not refreshing in Manual Tune
In Manual Tune, the user interface is not refreshed when the Resolution table editor is moved.
Click between the tabs to refresh the user interface. (SCR 9327)
Changing the Resolution Table can cause a loss of communication
Changing the Resolution Table on-the-fly in Manual Tune during a Scheduled MRM™ algorithm
acquisition causes communication to be lost with the instrument. You must restart the Analyst
software and AnalystService to regain communication. (ST 9771)
Syringe pump error not clearing if ignored
On the 5500 series of instruments, when the syringe pump reaches the stopper, a syringe pump
error appears. If you ignore the error for an extended period of time, and you continue clicking
through the Analyst software, the error will return but you may not be able to clear it as the Clear
Error button may be unavailable. To clear the error and regain communication with the syringe
pump, you can deactivate and reactivate the hardware profile. If the error is not cleared, then
restart the computer. In rare cases, you will have to deactivate the hardware profile and then
restart the computer and the instrument. (ST 9880)
Display graphs may be slow to update when running the 12 000 Da/s scan speed in
Manual Tuning mode
When running the 12 000 Da/s scan speed in Manual Tuning mode, the displayed graphs can be
slow to update and the Analyst software may appear to stop responding. This is especially true if
the user switches applications and then switches back. However, the data is collected
successfully and the program will update when the scan stops.
On the QTRAP® 5500 LC\MS\MS system, masses greater than 1000 Da can be
entered in the Isolation and Excitation tables
Although the mass range for the linear ion trap is 50 to 1000 Da, the software allows you to enter
values for masses greater than 1000 Da in the Isolation and Excitation tables. The effect of
entering additional rows for masses above 1000 Da is unknown but will likely affect the quality of
data for the entire mass range and users are encouraged to avoid doing this. (ST 11622)
On the QTRAP 5500 LC\MS\MS system, after performing a fresh installation of the
Analyst software, reference tables may appear empty
To avoid this issue, activate a hardware profile before attempting to edit a reference table.
(ST 8788)
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Acquire — IDA and IDA Method Wizard
IDA not triggering properly for Scheduled MRM basic methods
If a Scheduled MRM basic method is created from a Scheduled MRM advanced method, the
information from the additional columns in the advanced method remain and are stored in the
basic method. If the Scheduled MRM advanced method contained information in the Group
column, this information will be used by the IDA algorithm in the Scheduled MRM basic method
even though it should not be applied.
To avoid this, create a new Scheduled MRM basic method. If you want to convert an existing
advanced method into a basic method, copy all the mass table parameters from the advanced
method into a spreadsheet (such as Excel), delete the unnecessary columns, save the
spreadsheet in .csv format, and then import the .csv file into a new basic method. (AN-300)
MS3 isolation always uses the new LIT resolution table
In the IDA (Information Dependent Acquisition) Method wizard, although the choices for the
Resolution Q3 field (High, Unit, Low, and Open) are available for the MS3 scan type, the MS3
scan type always uses the LIT resolution table for Resolution Q3. The choices available for
Resolution Q3 are ignored. (SCR 11378)
Set to never exclude former target ions from IDA
If a quadrupole mass spectrometer profile is activated in the IDA wizard and you want to set the
Exclude Former Target Ions of IDA Criteria page to Never, select the For 0 secs option. (SCR
11762)
IDA not triggering on specific charge state
In the second level IDA, MS3 can be triggered by an ion of unknown charge state although the
charge states are specified as the criteria at this level. (SCR 11551)
DP and CE values not stored in final method
When IDA methods including MS3-dependent scans are generated using the IDA Method
wizard, DP and CE values specified for the survey and other dependent scans are not applied to
MS3 experiments. Type DP and CE values for MS3 experiments in the acquisition Method Editor
after you have created the method. (SCR 12463)
Doubly charged ions are sometimes incorrectly recognized as singly charged ions
Doubly charged ions are sometimes incorrectly recognized as singly charged ions in an EMS
survey scan of an IDA experiment. (ST 14677)
Singly charged masses are occasionally misidentified
In IDA experiments, singly charged ions are occasionally identified as undefined charges.
(17100)
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Undefined charge states are sometimes incorrectly recognized as singly charged
charge states
Undefined charge states are sometimes incorrectly recognized as singly charged charge states
in an EMS survey scan of an IDA experiment. (ST 17100)
In an IDA method, if a dependent scan experiment is deleted, an additional mass
range may be added to the survey scan
Refreshing the UI by clicking in a different field, switching between the experiments, or saving the
method will delete the added mass ranges. (ST 17047)
On the AB SCIEX QTRAP 5500 system, ER scans in IDA methods must have a
mass range less than 1000 Da
When you create an IDA method with a quadrupole survey scan and a confirmation scan
(Enhanced Resolution), you cannot have a survey quadrupole mass range greater than 1000 Da.
You will be prompted to lower the mass range or remove the confirmation scan.
On the AB SCIEX QTRAP 5500 system, occasionally this message appears “No
dependent parameters are found in the IDA method the file will open using
Explorer” when opening non IDA samples in data files collected at 12000 Da/s
The data file opens normally so you can ignore the message. (ST 13169)
Survey scan mass ranges are duplicated when users create an IDA method using
the IDA wizard
To prevent this issue from occurring, do not go back to previous pages in the wizard.
Alternatively, delete any duplicate ranges in the final method. (ST 17059)
IDA Method Wizard does not allow the user to select RF/DC scan rates for the
AB SCIEX Triple Quad™ 5500 system
The RF/DC scan rates are currently unavailable in the wizard. The final method that the wizard
creates uses the preset scan speed of 200 Da/s. This method is editable and can be saved with
the new scan speeds. (ST 9272)
Mass shifts of up to 1 Da may be observed for data generated using the IDA Wizard
for AB SCIEX Triple Quad 5500 system users only
When creating a method through the IDA Wizard, the scan speeds are not available for selection;
however, the scan time is available and is editable and is populated in the final method. The final
method defaults to 200 Da/s, however, the specified scan time may not necessarily correspond
to this scan speed. As a result, data collected with these methods may result in an observed
mass shift in the data. To overcome this issue, you can select a different scan speed, or if you
want to use the 200Da/s scan speed, select a different scan speed, switch back to 200 Da/s if
required, and then save the method before running it. (ST 19703)
Looping opposite polarity EMS experiments as survey scans in an IDA experiment
sometimes results in dependent data to not be triggered
The following scenarios prevent dependent data from being acquired:
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Notes on Use, Known Issues, and Limitations
•
EMS+ve > EMS–ve > ER > IDA Criteria > Dependent scans
•
EMS+ve > EMS–ve > IDA Criteria where charge state confirmation is selected to
NOT include unknowns > Dependent scans
Therefore, to allow dependent data to be acquired, either remove the ER scan type from the
method or check the IDA criteria to allow acquisition of unknowns. The latter scenario, however,
allows dependent scans to be performed only on undefined charge states. The peaks with the
specified charged states are ignored even if they satisfy all the other IDA criteria. (ST 17045)
No dependent scans are performed for an IDA method which includes a
quadrupole (–ve) > EMS (+ve) > dependent scan (+ve)
No dependents scans are triggered for data acquired with this type of method with or without a
confirmation (Enhanced Resolution) scan type and with or without “Unknowns” selected for
charge state confirmation. (ST 18132)
Incorrect ions selected for confirmation scan
An IDA method with a Scheduled MRM algorithm scan type as a survey scan and a confirmation
scan type does not work as expected if the intensity threshold in the IDA Criteria is set to 0. The
IDA method selects the ions from a future retention time window for the confirmation scan during
the acquisition over the ions that were satisfying all the IDA Criteria. To avoid this issue, set the
Intensity threshold > 0. The IDA method will work as expected. (ST 18941)
IDA acquisition fails if the hardware profile contains an ADC device
Restart all the peripheral devices and restart the Analyst service. To avoid this issue, do not
include an ADC device in the hardware profile if you will be performing IDA acquisitions. (ST
16102.)
Acquire — Method / Batch Editor/Queue Manager
File Information might show Scheduled MRM experiments as MRM if they are not
the primary experiment
If the user creates a multiple-experiment method with Scheduled MRM as not the primary
experiment (for example, EMS > Scheduled MRM > IDA > EPI), the File Information might show
the Scheduled MRM algorithm method as being an MRM method. Because of this, the
Scheduled MRM field will show “No,” the Target Scan Time field will not be shown, and Dwell
Time will be shown instead of Retention Time. (AN-232)
Scheduled MRM Pro: File Information shows 0.0 if Window field left blank in the
method
When creating a Scheduled MRM Pro method, users can enter a value for Window to supersede
the MRM Detection Window set in the method. If users choose to leave this field blank (the
transition will use the MRM Detection Window), the File Information will show 0.0 in the Window
column for that particular transition. (AN-270)
Analyst® 1.6.2 Software
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Release Notes
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Notes on Use, Known Issues, and Limitations
Users should not turn on the SelexION™ system during an acquisition
If the user turns on the SelexION system during acquisition, the currently acquiring sample is
aborted and the system briefly goes to an Error status. When the system recovers to the Ready
status, if users attempt to reacquire their sample, there is no indication that the system has
changed. Because of this, there might be a mismatch between the status of the system as shown
in File Info and the actual status of the system. Users should refrain from turning on or off the
SelexION system during acquisition. If this happens, new acquisition batches should be
submitted, rather than using the ‘reacquire’ function in the software. (AN-115)
Error is shown when using invalid characters in sample names
If the user enters a forward slash in a sample name within a batch, upon attempting to submit the
batch the error: “Invalid character found in path (/).” If the user enters other invalid characters (:,
“, <, >,?, |), the error will be “Invalid character found in path (: “< >? |)” is shown. (AN-94)
Pasting data into the batch editor
While the Batch editor supports copying and pasting from and to applications such as Microsoft
Excel, users should be aware that the batch editor contains columns that are hidden by default,
for example, Sample ID, Dilution Factor, and so on. When text is pasted from a spreadsheet into
the Batch editor, all columns are populated in sequence, whether visible or not. Therefore, it is
possible for data to be pasted to an unintended column.
If users want to paste data in to the Batch editor, they should manually expose all columns first,
to make sure that data is pasted as intended. Alternately, the user must make sure that the data
they are pasting in the Batch editor contains information for all columns, visible and hidden.
(AN-216).
TDF Scans removed for the 5500 instruments
TDF scans are no longer supported for the 5500 series of instruments. The 4500 series of
instruments do not support this scan type either. If users attempt to submit a batch in the Analyst
1.6.1 software, which uses methods containing TDF scans (created in a previous version of the
software), the acquisition will fail and an error will be logged in the Event Log.
Method duration may change when cycling between tabs
When users switch tabs in the Acquisition Method Editor, fields are recalculated. As a result, if
the user sets a method duration and then cycles between the Advanced MS and MS tabs, the
duration may change slightly as the number of cycles is recalculated. This results in a method
duration that best fits the number of actual cycles. (TT 34574)
Analyst software may stop responding if external valve is in hardware profile but
is not used in method
When configuring an external valve in the Hardware Profile, users must make sure that the valve
is assigned a proper switching method in the acquisition method. If users submit a method that
does not contain a valid valve switching method, the Analyst software may stop responding
during acquisition. If the valve will not be used during acquisition, it should be removed from the
hardware profile. (TT 34645)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Notes on Use, Known Issues, and Limitations
Number of Scans to Sum may be reset to 1
When using the MCA data collection, if the user sets the Number of Scans to Sum field and then
switches to the Advanced MS tab and back, the field may reset to 1. When using the MCA data
collection, users should set the Number of Scans to Sum field as their last step before saving the
method. (TT 34787)
DFT scans may fail to maintain targets
In some cases, users may see Dynamic Fill Time (DFT) scans overshooting the target intensity.
In these cases, users should switch to fixed fill times. (TT 34872)
Method Editor: Calculated Cycles not immediately updated
When changing the parameters that affect the method duration, the Calculated Cycles field is not
immediately updated. If users switch to the Advanced MS tab and back, they will see the field
updated. (TT 34884)
Simulation mode: Some methods may not end at expected times
When running acquisitions in the simulation mode (for testing new methods and so on), some
methods may not end at the expected time. The mass spectrometer should never be simulated
for real LC data acquisition. (TT 34893)
Dynamic Fill Time may not work in Manual Tune
When users run Manual Tune with DFT enabled, changes to compound parameters may not
trigger DFT to recalculate fill times. Therefore, when running Manual Tune, users should use
Fixed LIT fill times. (TT 34905)
DBS is not applied when a single MRM is acquired
When running an experiment containing a single MRM transition, Dynamic Background
Subtraction (DBS) is not applied, whether or not the feature is turned on. (TT 35242)
Queue: Waiting samples are treated as Acquired when the Queue stops
When the queue stops (acquisition completed, acquisition error, and so on), any samples that are
in the Waiting state are treated as acquired. If the Queue Options are set to show only a limited
number of completed samples, these waiting samples may be deleted from the queue. To avoid
this, increase the number of completed samples shown in the queue. (TT 35286)
Queue: Pause Sample Now ion not available
The Pause Sample Now icon on the Queue toolbar is inactive and will not affect acquiring
samples. (TT 35287)
Queue: Next Period button not available
The Next Period icon on the Queue toolbar is inactive and will not affect acquiring samples. (TT
35288)
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Release Notes
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Notes on Use, Known Issues, and Limitations
Sample Details from right-click menu show incorrect information
Selecting Sample Details from the right-click menu shows incorrect information (Sample Name,
Status) for samples with the status of Terminated or Partial. Sample details are available for
waiting and acquired samples. To see the correct information for terminated or partially acquired
samples, double-click the row. (ST 31086)
Columns cleared in the Queue Manager cannot be selected again
If users right-click in the Queue Manager, select Column Settings, and then clear the check
boxes, the columns are removed from the Queue Manager. However, the right-click menu is
subsequently not available and the columns cannot be restored to the Queue Manager. To avoid
this issue, do not remove columns from the Queue Manager. (ST 031088)
Moving and then deleting a batch causes the Analyst software to stop responding
In the Queue Manager, if a batch is moved and then deleted, the Analyst software will stop
responding. To avoid this issue, delete the batch without moving it. (ST 31098)
Unable to delete the last row when there are more than the maximum limit of MRM
transitions in the acquisition method
When pasting more than the maximum limit of MRM transitions in the acquisition method, you
cannot delete the last row. You can delete row n-1 and then edit the last row to include the
information that was just deleted. (ST 6968)
Note: For systems other than 4500, 5500, and 6500 series of instruments, 300 MRM
transitions are the limit when acquiring MRM data and 1000 MRM transitions are the
limit when acquiring Scheduled MRM algorithm data. For the 4500, 5500, and 6500
series of instruments, 1250 transitions are the limit when acquiring MRM data and 4000
is the limit when acquiring Scheduled MRM algorithm data. (ST 6968)
Copying and pasting acquisition methods
Copying compound dependent cells that are partially exposed in a mass ranges table may cause
the pasting action to result in an error. Highlight all cells completely (drag the mouse all the way
to the right) before copying them. Also make sure to copy into the same column for which the
selection has been made, otherwise incorrect data and/or errors might result.
Copying and pasting to mass table
See the Help for instructions when copying and pasting to the mass ranges table from one
acquisition method to another or from an external file to an acquisition method.
Unable to modify and save number of cycles
If you edit any previous version of method (.dam) files, you may not be able to modify and save
the number of cycles the first time. Repeat the process again to save this information.
Scans unexpectedly set to sum to 1
If you set the scans to sum to greater than 1, clicking the Advanced MS tab and then clicking the
MS tab resets the scans to sum to 1. To store the value properly, type the value and save without
clicking the Advanced MS tab. (SCR 11446)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Notes on Use, Known Issues, and Limitations
Missing column headers in previous versions of batch files
If you open a batch file created from an earlier version of the Analyst software, column headers
may disappear in the Batch Editor. (SCR 11578)
Source/gas information may not reflect values set as defaults in parameter
settings
When you create an acquisition method manually or through the IDA Method wizard, review and
update the Source/Gas parameters as appropriate. (SCR 11662, SCR 11711)
Unable to save or submit batch with long file path
You cannot save or submit an acquisition batch if its project path is longer than 126 characters.
When you submit this type of file, you will receive the following error message: “Failed to set
Header data”. When you save this file, you will receive the following error message: “Failed to
save BatchName”.
Pasting columns in mass ranges table
Pasting of individual column of values for compound dependent parameters in MRM and
Scheduled MRM algorithm methods from an external .csv or .txt value may not always work. You
must copy and paste the whole Excel sheet with updated dependent parameter values.
Pasting rows in mass ranges table
Pasting more than 300 lines into an MRM mass table could take several minutes.
Issue with importing file with MRM transitions
Make sure that the imported file is either a .txt (tab-delimited text file) or a .csv (comma separated
value) file. Make sure that the number of columns in the file is equal to the number of columns
revealed in the Analyst software method editor and that the column order matches. Also, make
sure that there are no empty cells in the file that you are importing. (ST 2717)
Error message appears when importing a text file into an MRM or Scheduled MRM
acquisition method
When importing a text file into an MRM or Scheduled MRM algorithm method, a message may
appear reading: “Invalid value entered into table. Please ensure only numeric values are
entered”. Although this message appears, the file is imported correctly. This issue is not
observed when importing .csv files or when copying and pasting from an external file regardless
of its format. (ST 019141)
Pasting into a mass ranges table during acquisition can cause the system to stop
responding
When pasting into a mass ranges table during acquisition, the Analyst software could stop
responding. You can only copy and paste into an MRM or Scheduled MRM algorithm table either
before or after acquisition.
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Release Notes
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Notes on Use, Known Issues, and Limitations
Switching valve tables must be populated before using method
When using a method containing a switching valve, make sure that the table is populated before
saving and using the method. If this method is used for acquisition, the system will stop
responding and you will have to restart the instrument. (ST 9431)
Pause time doubles when creating a quadrupole experiment after switching
between LIT and quadrupole scan types in the Method Editor
When users create a method containing a quadrupole scan type with a mass range of, for
example, 1000 to 1250 Da and then switches to an LIT scan type and then back to the original
quadrupole scan type, the pause time nearly doubles. To prevent the pause time from doubling,
do not change scan types during method creation. (ST 11465)
During batch creation, pressing Tab creates another row
When you create a batch, if you go to the last row in the Batch Editor and then press the Tab
button, another row is created. After the row is created, the Auto-Increment or Fill-Down
functionality does not work with this row. Also, any rows appended to your batch will appear
before this one. When you submit your batch, this phantom row will not be submitted. If a user
creates a batch with this extra row, the sample specified in this row will not be collected. Avoid
the use of the tab button to add rows to the batch; use the Add Samples button instead. (ST
14024)
Samples in a batch remain suspended after instrument error is corrected
The batch must be resubmitted to the queue to continue. (ST 16247)
Invalid ion energy in EMS scans
Although Ion Energy 1 is accessible in EMS scans, it is not applicable and should not be used.
(SCR 11764)
Acquire — Scheduled MRM Algorithm
Scheduled MRM algorithm experiment limit
For mass spectrometers other than 4500, 5500, and 6500 series of instruments, to maintain
optimum system performance, a Scheduled MRM algorithm, non-IDA experiment should not
exceed 1000 transitions and three dependent parameters. A Scheduled MRM algorithm, IDA
experiment should not exceed 1000 transitions and two dependent parameters. If the experiment
exceeds these limits, the Analyst software may stop responding and you will need to restart the
instrument and reactivate the hardware profile. You may reduce the number of transitions if you
want to increase the number of dependent parameters.
For the 4500, 5500, and 6500 series of instruments, the limit is 4000 transitions with four
parameters (CE, DP, EP, CXP).
Multi-period Scheduled MRM™ algorithm experiments not supported
Multiple period Scheduled MRM algorithm experiments are not supported in the Analyst
software. You cannot create these methods.
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Notes on Use, Known Issues, and Limitations
In certain cases there may be a decrease in sensitivity on the API 5000 instrument
when using Scheduled MRM algorithm as compared to MRM
This issue may be observed for experiments covering a wide range of Q1 masses over several
hundred Da. Keep this in mind when using the Scheduled MRM algorithm functionality on the
API 5000™ instrument. (ST 15149)
Batches containing the maximum number of Scheduled MRM algorithm
transitions and three mass dependent parameters where one of them is EP causes
the system to stop responding
Batches containing the maximum number of Scheduled MRM algorithm transitions and 3 mass
dependent parameters, DP, CE, and EP, causes the system to stop responding. To avoid this
occurring, do not include EP as one of the mass dependent parameters. (ST 16066)
Scheduled MRM algorithm parameters cannot be changed on-the-fly
Compound-dependent parameters for an acquisition method using the Scheduled MRM
algorithm may not be applied when changed in real time in Manual Tuning. When changing
parameters for a Scheduled MRM algorithm method in Manual Tuning under Tune and Calibrate
mode, the method should be stopped between adjustments and then restarted. (ST 9436)
Modifying Scheduled MRM algorithm mass ranges table can take several minutes
Modifying a Scheduled MRM algorithm mass ranges table with 2500 MRM transitions could take
several minutes. (ST 5251)
Acquire — Network Data Acquisition
Copy data to a network location before validating the checksum
If the user attempts to validate the checksum of a large file that is being acquired to a network
location, it is possible that the Analyst software will stop responding or will result in a failed
checksum. This is because network interruptions might cause a delay in writing the full file to the
network and require the AnalystService and client to be restarted. Alternately, the file itself might
become corrupted. Users should make sure that the file has been fully copied to the network
location before attempting to validate the checksum. (AN-202)
Potential loss of data when acquiring from multiple instruments to same data file
Do not acquire data concurrently from multiple acquisition workstations to the same network data
file.
Windows reporting Delayed Write Failed
On Windows XP, while the Analyst software is acquiring data to a network computer, Windows
may display an error dialog stating Delayed Write Failed at the bottom right corner of the screen
when there is a network interruption. This error does not prevent files from eventually being
transferred. Do not restart your computer at this time because Windows is still transferring files.
For more information, see the Microsoft Web site at:
http://support.microsoft.com/default.aspx?scid=kb;en-us;330174.
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Notes on Use, Known Issues, and Limitations
The Analyst software prompts you to re-enter root directory path
The root directory must follow the Universal Naming Convention (UNC) format: \\computer
name\drive name. Now mapped drives are converted automatically to full UNC paths. Full
network path lengths must be limited to 128 characters.
Network data security mode
For network data acquisition, work in Mixed Mode or Integrated Mode security. If you use Single
User Mode, make sure that you are a network domain user with read/write access to the project
folder. (SCR 11781)
Cannot access current data
If you are using network acquisition, you cannot see the acquired data from a remote workstation
until the sample is finished.
No audit trail record when the network is down
When the network is down, the data file creation and other non-processing activities performed
during data acquisition only are not recorded in the audit trail database, which is not accessible.
You can add steps to your Standard Operation Process (SOP) to check with your IT department
regularly if there has been any network interruption during previous data acquisition processes
and to avoid data acquisition during network maintenance work. You can also review the
Windows application event log to check for any network disconnection warning events. All
relevant acquisition data is still logged in the data file even if the network is down. (SCR 11648)
Slight time delay due to file transferring
When data files are acquired to the network, the time reported in File Info in Explore mode for
Last Sample Finished is the actual time the file was copied to the network, which may differ from
the time of acquisition of the last sample. This is due to the delay when transferring files to the
network. (SCR 9523)
Verify checksum after file transfer complete
When you click Verify Checksum on a file that has just finished acquisition, checksum may
intermittently fail if the data file transfer to the network is in progress. Checksum will work after
the transfer is complete. (SCR 11419)
Invisible subset file
When you make a subset of a sample file on the network, the file name may not be visible until
after you restart the Analyst software. (SCR 11729)
Long wait period if you have no write access
If you do not have write access to a network project and try to open a data (.WIFF) file, you may
experience a long waiting period while the audit trail process tries unsuccessfully to update the
information. (SCR 9906)
File transferring fails due to limited space on the network
When acquiring to the network server with user-specific space limitations, the Analyst software
may not be able to detect the remaining space available. As a result, the data transfer process
Release Notes
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Notes on Use, Known Issues, and Limitations
may fail, but acquisition is not impaired. The data remains on your local acquisition workstation.
(SCR 11420)
Spectral arithmetic output file not saved
If the root directory is on the network, select Open the New File Immediately in the Analyst
software under the Output Filename section in the Spectral Arithmetic Wizard–step 4. Otherwise,
the output file may not be saved. (SCR 11746)
Explore
CAD gas setting displayed incorrectly in file information
If a data file was acquired using simplified CAD gas settings and opened in the Analyst software
without the correct hardware profile active, the CAD gas setting in the file information will be
displayed incorrectly. A CAD gas setting of Low will be displayed as –1, Medium as –2 and High
as –3. (AN-299)
Processing large data while performing long data acquisition
Avoid processing (for instance, performing XIC) a large data file that has more than 600 MRM
transitions while performing a long data acquisition. Doing so may cause the software to become
unstable and data to be lost. Use another computer to process such data. If you need to open the
currently acquiring data, the display for currently acquiring Scheduled MRM algorithm data
defaults to TIC to open the file faster. Processing these files should still be kept to a minimum
during acquisition.
Processing Options truncates non-Integer values
The Analyst software Processing Options / Integration screen (Tools > Settings > Processing
Options, Integration tab), allows you to enter decimal values between 0 and 100. However, once
the screen is closed and reopened, these values truncate to their integer values.
“Subtract Range Locked” option appears to be active; menu item in the rightmouse menu does not update
When right-clicking on a chromatogram, the feature appears to be enabled whether or not it
actually is. To see whether or not the feature is enabled, see either the Menu bar (Explore >
Background Subtract > Subtract Range Locked) or the Explore Toolbar. If the icon is displayed as
depressed, the feature is enabled.
Unable to sort Peak Lists properly
In rare instances, the Peak List does not sort properly. To restore functionality, close the Peak List
(deleting the pane) and re-open it.
Cursor does not correspond to the time point of the spectral data
Occasionally, the cursor is incorrectly allowed to be placed between data points. The time in the
header of the spectrum of the active chromatogram is always correct.
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Release Notes
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Notes on Use, Known Issues, and Limitations
Missing data when exporting to PDF format
When the Analyst software is active with several panes open, exporting the active window to a
PDF file may not export all data from the window. Use Export when there are only a few panes in
the window.
Time range discrepancy for Contour plot
When saving a processed data file (PDT) with a Contour plot shown, the saved file displays a
different time range from the original Contour.
X-axis not extended
After offsetting a chromatogram, the x-axis (time) range is not extended to include the shifted
data.
DAD margin for negative absorbance not functioning
The diode array detector (DAD) margin for negative absorbance does not function.
Performance degradations due to large number of scans
Processing data can be slow when the data file contains a very large number of scans resulting
from the use of short dwell times. Keep the number of scans below 30,000. (SCR 7964)
Viewing IDA data files
If you open an IDA experiment data file while acquiring, it displays in Explore mode even if the
IDA Explorer is set as the default viewer in the Appearance Options dialog. If you open the data
file after acquisition, it displays in the IDA viewer. Samples that were opened in Explore mode
during acquisition do so by default when the acquisition is complete as well. You can open the
sample in the IDA Viewer if you reopen the file. (SCR 9805)
Integrated Harvard syringe pump not in file info
In some cases the File Info in Explore mode indicates that the integrated Harvard syringe pump
was not used even though it was used. (SCR 8643)
Smoothing does not consider 0 intensity points
The Smoothing function does not consider 0 intensity points. Holes might appear in the spectrum
after smoothing if there are intensities of 0 in the data file. (SCR 13204)
Show File Information
Opening the File Information pane using the Show File Information command may cause the
software to stop responding or to omit information from the display. This is an intermittent display
problem and no data is lost. If this occurs, configure the Audit Trail Manager settings to No Audit
Map or alternatively deselect the Closed Module event in the Audit Map Editor to view or save
the File Information to a file. The original audit trail settings should be restored. Only an Analyst
software Administrator has the privilege to configure the audit trail settings.
Overlay on plot for isotopic distribution in calculator
Occasionally, this feature does not function as expected, however, the text will still be accurate.
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Notes on Use, Known Issues, and Limitations
Incorrect status in File Information
On the 5500 series of instruments, the file information incorrectly shows the status as “Bad” for
the Curtain Gas™ flow and interface pump. There is no interface pump on the 5500 systems.
Also, although the file information will read “Bad” for the Curtain Gas flow, this does not
necessarily reflect the status at the time of acquisition. If during acquisition, the Curtain Gas flow
status develops to a true “Bad” state, then acquisition for that sample will stop with an error. (ST
8853)
Delay in displaying sample list
On the 5500 series of instruments, it takes more than 90 seconds to populate the sample list for
a data file acquired with more than 1000 samples. Allow for at least 90 seconds to populate the
entire sample list. If you acquire more than 1000 samples into a .wiff file, it will take at least 90
seconds to populate the sample list. The Analyst software will be able to open the file; however,
we recommend that you acquire the samples into different data files, if possible.
Syringe pump method information missing from the File Info
On the 5500 series of instruments, the syringe pump details used to collect the data are not
displayed in the File Information pane for data where a syringe pump was used. You should note
which flow rate and syringe diameter were used during acquisition. Alternatively, the user can
obtain this information from the data file by recreating the acquisition method from the file
information by right-clicking on the file information to select Save Acquisition Method. You are
required to have the same devices in your hardware profile to recreate the method completely.
(ST 7861)
Explore History file not displaying properly
The Explore History File does not display properly. The description of all the changes is
sometimes merged into one cell but it is often still legible. In some instances, some information
may be missing. (ST 9481)
Changes to offset in History pane not appearing
You must reopen the History pane to show changes to the offset. (ST 9486)
Reviewing MRM data changes the active XIC
When opening a saved Explore History File (.eph) from a Total Wave Chromatogram (TWC)
where the data from the mass spectrometer is MRM data, the displayed data is the overlaid XICs
but reviewing the changes will change the active XIC. The listed history, however, is correct and
can be used to manually apply those settings to the original data.
Occasionally, samples in data files collected at 12 000 Da/s cannot be opened
If this occurs, open the previous or any subsequent sample and use the forward and back arrows
to navigate to the sample that will not open. (ST 13169)
If you expand data in the IDA viewer while a sample is acquiring to the same data
file, data from an acquired sample is not displayed
No data is displayed in Explore mode for an acquired sample if you expand data from the IDA
Viewer while a second sample is being acquired to the same .wiff file. (ST 18228)
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Notes on Use, Known Issues, and Limitations
Undocked Graph Information Window may cause the software to stop responding
Occasionally when the Graph Information Window is opened and undocked the software stops
responding. This is especially the case when the window is left open and undocked for several
hours while acquisition and processing take place. To avoid this issue, keep the Graph
Information Window docked. (ST 16700)
The Q1 resolution offset table at 10 Da/s is missing in the File Information
The Q1 resolution offset table at 10 Da/s is missing in the File Information for a negative ER scan
type. This does not affect the data or any future acquisition. To retrieve this information, you may
look into a data file acquired in Q1 negative mode. (ST 13331)
Sections of ions appear to be missing in EPI scans
On the 5500 series of instruments, when you use Q0 trapping, a fill time of at least 20 ms is
required. EPI spectra acquired with a Fill Time less than 2 ms will result in a missing range of
ions in the second mass range when Q0 trapping is On. In general, you can expect to see an
overall decrease in sensitivity even with one mass range under these conditions. (ST 8200)
Compound Library databases with over 20 000 entries fail to display full
information
When opening Compound Library databases that have over 20 000 entries, the individual fields
will not display the full information used to populate the original database; “NA” is populated
instead. The recommendation to overcome this issue is to re-save the original database into two
separate databases in order to be able to view all entries and then populate future entries in a
new database. For example, delete the last 10,000 entries and save this database as “Part 1”
and then reopen the original database, delete the first 10,000 entries and save this database as
“Part 2”. Note: Deleting entries and then adding new ones is not recommended. (ST 19297)
The Analyst software stopped responding during real-time XIC data extraction
When large numbers of ions were extracted in real-time during acquisition using an MRM or
Scheduled MRM method, the Analyst software may have become unresponsive. This issue has
been corrected. However, users should be aware that there may be cases where extracting large
numbers of chromatograms will still cause the software to slow or become unresponsive. For
example, having multiple XIC panes open simultaneously, or acquiring data from multiple
methods to the same .wiff file. In these cases, users should refrain from extracting
chromatograms in real-time. (AN-292)
Make Subset File feature and script do not support checksums
When using the Make Subset file in the Explore menu or the Make Subset File script, the
checksum of the file being used is not checked and the resulting file will have a valid checksum
even if the starting file has an invalid checksum. (AN-297)
Explore — Library Search
Blank results in new field
When performing a Library Search from an open spectrum, if you click View Manager from the
Search Results window and add a new field, the results for this new field might appear blank.
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Notes on Use, Known Issues, and Limitations
Clicking on the field a few times, will cause the results to appear. This is a graphical issue and
does not affect functionality.
Hidden column in Compound Library view
When viewing the Compound Library, increasing the width of the last column may uncover a
column named Hidden, with populated values. This is a graphical issue and does not affect
functionality. Do not modify the data in this column. (ST 3165)
Editing the compound name twice may cause the Analyst software to stop
responding
If you edit the name of a compound in the library, click OK, and then attempt to edit the
compound again, the Analyst software stops responding. To avoid this, after clicking OK to
change the compound name, close and re-open the library before attempting to change the
same compound. (ST 2283)
Opening a library record in the default library may show a blank spectrum
If this occurs, reconnect the library database (Tools > Settings > Optimization Options > Library
Manager) to correct the issue. (ST 1860)
Explore — WIFF Data File
Analyst software file compatibility
The Analyst software is fully backward compatible. However, it is not forward compatible, that is,
Analyst 1.5 software data files, for example, do not consistently open in Analyst 1.4.2 software or
older versions. If you upgrade acquisition computers to the newer Analyst software, you should
also upgrade processing computers to the same version.
Flat file size limit
The software can display data in the flat file (.WIFF.scan) for files up to 2 GB in size. Any data
stored beyond this limit may not display properly. In addition, larger file sizes may degrade overall
performance. Begin acquiring data to a new data file if your file size nears this limit (for example
at 1.5 GB).
Quantitate
Accuracy values may be different between different versions of the Analyst
software
In the Results Table, the Accuracy values may be different between Analyst software versions
1.5.x and 1.6, for the results created using same samples – data files. In the Analyst 1.6
software, accuracy values are rounded to 13 decimals. In some cases, the difference on the10th
decimal may be observed. (ST 33935)
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Release Notes
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Notes on Use, Known Issues, and Limitations
Zero Accuracy values display as N/A in previous versions of the software
Zero Accuracy values 0.00 were displayed as “N/A” in previous software versions. In the Analyst
1.6 software, if the calculated accuracy value is 0.00 (up to 13 decimals), that value will be
displayed as a number (0.00). (ST 33935)
Discrepancy in Results Table file size
Depending on the number of samples, the Results Table file size may be larger than in the
previous version of the Analyst software. (ST 33496)
Incorrect printouts if manual integrations are not accepted
If the user performs a Manual Integration and attempts to print the window or workspace without
first “accepting” the changes (or completing an e-Signature if required), the resulting printout may
be incorrect. The user will see two Results Tables printed showing the areas before and after the
manual integration, instead of the selected Results Table and chromatogram. If after performing
a manual integration, the user “accepts” the change (or completes an e-Signature) or navigates
to a different selection, the Print > Window and Print > Workspace commands will function as
intended.
Algorithm compatibility
Scheduled MRM algorithm data cannot be analyzed with Analyst Classic or previous versions of
the IntelliQuan (IQA/MQ II) algorithms. For this reason, the IntelliQuan integration algorithms
have been improved to support Scheduled MRM algorithm data, and have been renamed IQA II
and MQ III. For more information, see Technical Information Regarding Integration on page 99.
Due to this change, several behaviors will be observed in the software:
•
When creating a new quantitation method with Analyst Classic as the preset
algorithm, the software warns about algorithm incompatibility and the new method
uses IntelliQuan-MQ III instead. This operation has no affect on the preset algorithm.
(ST 5388)
•
IntelliQuan Results Tables from versions of the Analyst software earlier than version
1.5 will continue to use the previous versions of the algorithms in the Analyst 1.5
software so that the results presented are consistent. This is the only situation in
which previous IntelliQuan algorithms are used in the Analyst 1.5 software.
•
The Quantitation wizard cannot create a quantitation method for a data file that
contains more than 94 transitions. Before you can use the Quantitation Wizard to
generate a Results Table, you must first create the quantitation method using the
Build Quantitation Method feature. Select this quantitation method on the Create
Quantitation Set - Select Method page of the Quantitation Wizard. (ST 5919)
•
Previously generated quantitation methods with the Analyst Classic algorithm cannot
be used to analyze Scheduled MRM algorithm data. To carry forward the
information, export the method as text using the Create Text File from Quan Method
script and then re-import it using the Create Quan Methods from Text Files script.
Both scripts are provided on <drive>:\Program Files\Analyst\Scripts\All Mass
Spectrometers folder.
•
You cannot add Scheduled MRM algorithm data to Results Tables using Analyst
Classic or older IntelliQuan algorithms.
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Notes on Use, Known Issues, and Limitations
IQA II Integration algorithm occasionally does not find peaks on Scheduled MRM
algorithm data
For Scheduled MRM algorithm data, it is highly recommended that you use IntelliQuan - MQ III
as the default integration algorithm, as the peak is sometimes not found in the retention time
window when using Scheduled MRM algorithm with IQA ll.
IntelliQuan - IQA ll parameter-free integration algorithm not set by default
For regular MRM data, IntelliQuan - IQA II is the preferred default algorithm. For fresh Analyst 1.5
software installations, this must be set manually, as the MQ III algorithm is set by default. For
instructions, see the Help.
Default integration algorithms
Newly created projects always copy the default integration settings from the Default project. For
fresh Analyst 1.5 software installations, this preset is now IntelliQuan - MQ III. If you are reusing
your Analyst Data folder from a previous version, the preset from that Default Project will carry
forward to the Analyst 1.5 software.
Large signal-to-noise values sometimes reported in the Results Table
Occasionally, when very low or no noise is selected for a background, very large values to over
20 digits are reported. This might occur because there is no baseline noise for these cases. The
signal-to-noise should be reported as N/A in these cases. Readjust the selection of the baseline
to make sure that some baseline noise is applied to the signal-to-noise calculation.
Baseline Sub window
The IntelliQuan Baseline Sub window is actually a half window. The window used is twice the
width that is entered. This applies both to the Integration tab of the Processing Options and the
IntelliQuan Parameters dialogs opened by right-clicking in a data list. (SCR 12984)
Exporting with Sum Multiple Ions produces bad text file
Exporting a Results Table built with the Sum Multiple Ions option produces data in separate
columns. The values appear under incorrect headers and the text file may be incorrect. (SCR
10947)
Diode array detector results not removed
In a DAD Results Table, even when all DAD data is removed and an ADC data sample is added,
the DAD information remains in the Results Table. (SCR 7998)
Analyte mass range column displays N/A
If an automatic quantitation method is used to build a new Results Table, the Analyte Mass
Ranges column displays N/A instead of the actual mass range for the corresponding sample and
analyte (potentially all different). (SCR 8790)
Peak asymmetry error
When you create a Results Table and display Peak Asymmetry, the column shows 0.00 if no
peak is found. (SCR 10688)
Analyst® 1.6.2 Software
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Release Notes
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Notes on Use, Known Issues, and Limitations
Inconsistent last decimal digit
When opening a Statistics table for two Results Tables (by selecting Group By Concentration
from the Conc. as Rows box and selecting Area or Height from the Statistics Metric box), the last
digit for some of the statistical results (Mean) could be different depending on the order of
opening the data files. The same issue is seen in mean calculations as well. (SCR 13198)
Quantitation integration mass tolerance
The algorithm for selecting a particular MRM transition from the Q1 and Q3 masses stored in the
quantitation method operates as follows:
•
Analyst 1.4 software: The first transition ordered from lowest to highest for which
both the Q1 and Q3 masses are within a tolerance of 0.1 Da is selected. For
example, given two separate transitions, one with Q1 140.0 and Q3 of 134.0 and
another transition with Q1 of 140.1 and Q3 of 134.1, a quantitation method will not
be able to distinguish between the two transitions. Since the algorithm finds the first
transition within the 0.1 tolerance, the 140.0/134.0 transition will be selected both
times.
•
Analyst 1.4.1 software: This was changed to use a smaller tolerance of 0.0001 Da.
The reason for the change in the Analyst 1.4.1 software was to allow two transitions
with both Q1 and Q3 masses within 0.1 Da, but more than 0.0001 Da, of one another
to be quantitated. If you use the same example as in the previous version, 140.0/
134.0 and 140.1/134.1 are now valid. This allows two close transitions to be
distinguished; however, this did not take into account the mass tolerance values
used by users who apply the same quantitation method across instruments, each
with their own unique calibration.
•
Analyst 1.4.2 and newer software: The transition whose masses are closest to the
values from the quantitation method, but still within a tolerance of 0.1 Da, is used.
The software determines which transition is closest by summing the Q1 mass
variation and the Q3 mass variation (between the quantitation method and the
acquisition method) and then selecting the transition whose variation sum is the
smallest.
Quantitation of a sample with a large number of transitions will appear slow
For example:
•
Generating a Results Table on the recommended computer using one sample
containing 2500 transitions can take about three minutes. (ST 9944)
•
Creating or saving a quantitation method using Scheduled MRM algorithm data that
contains 2500 transitions can take up to 15 minutes. (ST 9944)
Adding a Formula Column causes the software to stop responding
If the user performs an operation using a Formula Column in a Summary Page in a Results Table
the software stops responding. To prevent this behavior, remove the 500s in the brackets in the
column names in the Formula field. (ST 12940)
Cancel button unresponsive when closing an unsaved quantitation method
When closing a workspace with an open, unsaved quantitation method, the Cancel button is not
responsive. To close the window without saving the method, click No instead of Cancel. (ST
15477)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Notes on Use, Known Issues, and Limitations
Analyst software stops responding when you export a Results Table to a
nonexistent directory
This occurs when the user specifies the incorrect path in the “File name” list by typing in the path.
Make sure that the path specified exists and is correct. (ST 15992)
Save As dialog points to incorrect folder
When users save a quantitation method that required a data file to open, the Save As dialog
points to the folder were the data file was located instead of the Quantitation Methods folder.
Browse to the appropriate folder before saving the quantitation method. (ST 16129)
A peak is not integrated as expected when increasing the RT window beyond 40
seconds
When you use the IQA II algorithm, RT windows larger than 40 seconds are ignored; even if the
user sets a window larger than this, a window of +/-20 seconds is effectively used. Either adjust
the expected retention time for the shifted peak or for batches where this is happening for many
samples, switch to the MQ III algorithm. (ST 17676)
Older versions of Quantitation methods may cause the software to stop
responding
When selecting a Quantitation method in a batch that was created with the Analyst 1.4.2
software, the Analyst software stops responding. To use quantitation methods from previous
versions of the Analyst software, save the methods using the Analyst 1.5.1 software and then
select them. (ST 18026)
Error when quantitating using TIC as Q1/Q3 selection
If you use the Quantitation wizard and specify the TIC as the Q1/Q3 selection, the Analyst
software displays an error when you advance the wizard. Click OK to successfully continue with
the wizard. (ST 3242)
Column sorting
Occasionally, sorting columns in tables does not produce repeatable results. Sort the index
column to make sure that sorting is always correct.
Quick Quant with full scan methods
In the Acquisition Batch Editor, creating a Quick Quant method causes inconsistent behavior if
the acquisition method selected is a full scan method. After saving this method, you cannot open
it. Quick Quant works as expected with all other scan types. It is recommended that you do not
use Quick Quant with full scan methods. (SCR 9866)
New Quick Quant methods do not apply new quantitation default values
New Quick Quant methods generated through Build Acquisition Batch do not use the modified
quantitation default values specified through the Quant Method Editor Settings dialog.
(SCR 6997)
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Release Notes
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Notes on Use, Known Issues, and Limitations
An intensity drop may be observed if running a Scheduled MRM algorithm
experiment with masses greater than 1000 Da
Avoid using masses above 1000 Da in Scheduled MRM algorithm experiments. In these
instances, we recommend using the MRM scan type. (ST 11772)
Some items unavailable under the Administrator role for the Quantitate module are
not honoured
Although the “Change default number of smooths (in Wizard)” and “Change concentration units
(in Wizard)” are not available for the Administrator under role-based security, a user with the
Administrator role still has access to these features in the wizard. (ST 19149)
The concentration units specified when building a quantitation method do not
propagate to the Results Table if different units are used per analyte
Although a user can enter different units for different analytes when building a quantitation
method, only the first set of units is used in the Results Table. (ST 19151)
Correct data displayed in the calibration window
The data in the calibration window may not be consistent with the Results Table if few peaks are
found in the Results Table. To correct this, refresh the window by saving it. (SCR 11282)
Analyst Software Reporter
Reporter Template Editor might not show the Tags panel for the Blank Template
When editing the Blank Template in Reporter, the tags panel might not be shown by default,
depending on the version of Microsoft Office used. If the panel is not visible, users can make it
visible by selecting View > Document Editor, followed by View > Document Actions. (AN-250)
Chromatograms are not shown if the Label field contains information
When creating a Reporter template, if the user adds a chromatogram and then types anything in
the label field for the tag, the printed report will not display the chromatogram. Make sure that the
label field is empty. (AN-255)
Reporter Template Converter: Unable to convert four templates
The Reporter Template Converter is unable to convert the following templates: Select Analyst 20
percent Report.xml, Sample Report with MRM ratios.xml, Sample Report with MRM ratios2.xml
and Sample Report with MRM ratios EU.xml. Users will receive an error message when
attempting to convert any of these templates. (AN-258)
Chinese characters might be unreadable in Reports
When using the Reporter 3.2 software to print reports using Chinese fonts, the spacing between
characters might be too small to allow the report to be easily readable. This might happen when
printing to Word or PDF formats. If this happens, select the option to print to HTML format, as this
format spaces the characters appropriately. (AN-131)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Notes on Use, Known Issues, and Limitations
Adobe Acrobat may stop responding after printing to PDF
If the user selects both options to Print to PDF and Print Automatically, after generating the
report, Adobe Acrobat will launch but will stop responding. If the user manually closes Adobe
Acrobat, the report will open automatically as a PDF. This is a workflow defect and does not
affect the generation of the actual report. (ST 35621)
Report names containing periods may cause the Reporter to crash
When creating a report, if the user specifies a filename that contains periods (‘dots’), they must
also specify the file extension. Failing to do so will cause an error to be generated: “Failed to
process the report file. Unsupported format requested.” For example, specifying a report as
“report 1.2.3” will cause a crash; whereas, specifying “report 1.2.3.docx” will generate the report
as intended. Note that the extension must match the format selected in the Reporter software.
(ST 35636).
Generating a PDF report might be slower for Windows 7 users
On Windows 7, if you are not an Administrator then the report will take longer to run. (ST 033975)
MS Office Requirements
For the Analyst 1.6.2 software, MS Office 2007, 2010, or 2013 is required to use the Reporter
functionality included with the Analyst software to edit reports.
Installer
Message appears during installation advising users to downgrade the firmware on
the 5500 series of instruments
If you have the 5500 Components Patch installed and you are installing Analyst 1.5.1 software,
you will receive a message instructing you to downgrade the firmware. Ignore this message and
continue with the installation procedure. Follow the instructions in the installation guide to
upgrade your application firmware. The installer will automatically uninstall the 5500 Components
Patch for you.
Smart Services runtime error
Occasionally, a Smart Services runtime error appears when installing or uninstalling the
HotFixes. Click through the error; the error does not affect the installation or removal of the
HotFixes.This error occurs only when Smart Services Mass Spec Gateway v 4.1 is installed. (ST
11498)
Other
Screen flickering
There may be some flickering when switching between modes and between windows in the
Analyst software. The flickering does not indicate a serious problem or potential shut down and
will not affect data. (ST 3614)
Analyst® 1.6.2 Software
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Release Notes
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Notes on Use, Known Issues, and Limitations
File Translator utility
The File Translator utility does not support the translation of Agilent MSD data to .wiff.
Changing power management settings on the Optiplex 960 is not recommended
Long delays (up to five hours has been observed) between samples in the batch may be seen on
the Optiplex 960 if the power management settings (C-State control) in the BIOS are changed.
This has not been observed for all scan types. (ST 18017)
Nebulizer Current status is not displayed correctly in the Detailed Status window
On the 5500 series of instruments, the Analyst software does not display the Nebulizer Current
correctly in the Detailed Status window while the instrument is in operation. A value of 0 appears
but this does not accurately reflect the actual applied current. Contact your FSE if no change in
performance is observed when you change the nebulizer current in the method or if you suspect
a problem with your nebulizer current.
Compatible Software
Automaton support discontinued
The Analyst software does not support the Automaton software. The Automaton software
package is replaced by the DiscoveryQuant™ software.
Some LightSight software versions cannot create GSH precursor ion IDA methods
LightSight software for metabolite identification is unable to create GSH precursor ion IDA
methods when the molecular weight of the molecule is above 550 Da. In version 2.0 and 2.1, the
LightSight software cannot create GSH Prec IDA methods and in version 2.2, the software
cannot create GSH Prec IDA and GSH Prec/NL IDA methods. LightSight software can create
GSH Prec methods for molecules with a molecular weight above 550 Da only if you do not create
an IDA method.
AAO Development Kit
For third party developers to develop with this version of AAO, they can find the AAO
Development Kit on the Analyst 1.6.2 software DVD in the \Extras\AAO folder. The kit contains a
User’s Guide, Release Notes, Source Files, Sample Code, and so forth.
When setting up a root directory for the Analyst Administrator Console, make sure
that the path name does not include the word “Projects”
When setting up a root directory for AAC (Analyst Administrator Console), make sure that the
path name does not include the word “Projects”. If the path name includes the word “Projects”, a
series of messages are returned to the user that prevent the user from logging into the Analyst
software through the AAC. The messages may indicate that the user does not have access to the
projects in the Workgroup to which they belong or that the projects included in the Workgroup do
not exist. Contact your administrator to rectify this issue. (ST 19394)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Notes on Use, Known Issues, and Limitations
Connection from AAC to the AAC server
Connection from the AAC to the AAC server should be made using the IP address and not the
AAC server name. (ST 31068)
Scripts
Users should not launch scripts from the Analyst software folder in Windows
Explorer
Some Analyst software scripts are available as .exe files within the Analyst software folders.
However, these scripts should not be launched manually. They should only be launched from
within the Analyst software. (AN-120).
Make Subset Script: Decompose function does not work
The Make Subset script has an option to decompose a file with multiple samples into individual
samples. This feature no longer works. (TT 35062)
On Windows 7, the Mascot script does not populate the file name automatically
On Windows 7 with Internet Explorer 8, the Mascot script does not populate file name
automatically. Users will need to select the file name manually using the Browse button. (ST
33797)
Moving the cursor over the graph can cause the MRM3 Optimization script to stop
responding
If you move the cursor over a graph that is not displaying correctly, the MRM3 Optimization script
stops responding. To avoid this issue, do not move the cursor until the script has finished
running. (ST 33987)
AutoQuant with Automatic Reports.dll script does not support Scheduled MRM
algorithm data
When running the BatchScriptDriver Script, if you select a Scheduled MRM algorithm data file to
be processed with the AutoQuant with Automatic Reports.dll script, an error message indicating
that samples are not compatible with the quantitation method appears. You can process MRM
data successfully. (ST 9052)
Label XICs script labels traces with zeroes
If you run the LabelXICs script using Scheduled MRM algorithm data, the XIC trace is labeled
with zeroes. The mass corresponding to each XIC can be found in the header of the data file. (ST
6109)
Mascot script fails to run for single EPI spectra
The Mascot script fails to run for single EPI spectra or for summed EPI spectra acquired with
MCA turned on. On the Explore menu, click Show TIC, highlight the entire TIC or highlight a
small region around the peak of interest and then run the Mascot script. By default, the search
option All MS/MS spectra from selected region(s) in TIC is selected. This option will run correctly.
(ST 8856)
Analyst® 1.6.2 Software
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Release Notes
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Notes on Use, Known Issues, and Limitations
Exclusion List cannot be imported into an IDA Method
The Exclusion List created from the Make Exclusion List From Spectrum script cannot be
imported in an IDA method. To make this work, you must enter headers in the list in the format
provided by the returned error message. (ST 2027)
Mass range for Q1 and Q3 scan data is not extracted
Occasionally, the XIC From Table script does not extract the entire mass range for Q1 and Q3
scan data. An error message appears indicating the mass ranges that can be extracted can
provide further guidance. Reopening the data file and restarting the script may also correct this
issue. (ST 9646)
Subsequent integrated area not appearing
When running the Manually Integrate Script to integrate consecutive peaks, the blue integrated
area is visible only for the first run of the script for the first peak; subsequent integrations using
the script do not show the blue area and the caption from the last integration remains. Reopen
the data file and run the script again to see the integrated area. (ST 9650)
Incorrect ramp information given for AF2 parameter
On the 5500 series of instruments, the MS3QuantOptimization Script reports the incorrect ramp
information for the AF2 parameter. The report shows that the AF2 parameter is ramped from 0 to
100 mV with a step size of 2 mV. The actual ramp range is 0 to 0.3 V with a 0.025 V step size.
(ST 9821)
AF2 graph is not always legible
Occasionally, the AF2 graph produced while running the MS3QuantOptimization script is illegible
during acquisition in the script user interface. This occurs only for graphs for which there is no
resulting spectral information. This does not affect the operation of the script. (ST 9822)
Starter method must have a syringe pump enabled for the MS3QuantOptimization
script
Make sure that the starter method has a syringe pump enabled. Open the starter method, if the
syringe pump has a cross, right-click to select Use to enable it and save the method. If the
syringe pump is not enabled, then the syringe pump will not run when the script is executed.
The Merge MRM Methods script causes the Analyst software to stop responding if
the hardware profiles being merged do not match
The Merge MRM Methods script causes the Analyst software to stop responding if the hardware
profile does not match the hardware profile used to create the methods being merged or if the
matching hardware profile is not active. To avoid this issue, make sure the hardware profile
activated in the Analyst software matches the active hardware profile for the MRM methods
being merged. (ST 17455)
Merge MRM methods script does not merge the Compound ID
Enter the Compound ID manually. (ST 2474)
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Notes on Use, Known Issues, and Limitations
Error when selecting “Subtract Control Data from Sample Data” on the Scripts
menu
Hold down the Shift key while selecting the script. An About dialog displays and the script runs.
(ST 6208)
The XIC from BPC script causes the Analyst software to stop responding
Do not use this script. (ST 6209)
Opening data created with Make Subset File script occasionally causes the
Analyst software to stop responding
Opening data created with the Make Subset File script occasionally causes the Analyst software
to stop responding when attempting to subset large data files. This is especially an issue when
trying to subset a data file with many samples and many MRM transitions. Do not use this script
with files acquired at the acquisition limits of 100 samples per data file and 1000 transitions in a
Scheduled MRM algorithm data file. (ST 6849)
Occasionally, error messages appear when running the Make Subset File script
Close the error messages if they appear; the script will still run correctly. (ST 18961)
Inclusion and Exclusion lists are not copied when IDA methods are converted
using the Convert Methods script
To avoid this issue, edit the masses in the Inclusion and Exclusion lists of the original method to
fit within the accepted range of the destination method. (ST 18986)
Methods with LIT scan types that have mass ranges over 1000 Da cannot be
converted to AB SCIEX QTRAP 5500 methods using the Convert Methods script
To avoid this issue, change the mass range of the original method to fit within the acceptable
range of the destination method. (ST 18670)
Convert Methods script
After you have created your method using this script, review the new method to make sure that
the method has been converted to your satisfaction.
Peripheral Devices
CTC PAL / Leap Devices
CTC software update
If you have applications that are using CTC SDK (for example, CTC Cycle Composer or CTC
Cycle Editor) that are older than 1.6.0.3, they may not work after the Analyst 1.6 software is
installed. Contact the manufacturer for the latest versions of the CTC software. (ST 32245, ST
33375)
Analyst® 1.6.2 Software
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Release Notes
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Notes on Use, Known Issues, and Limitations
Enabling/disabling barcode reading
The CTC PAL Autosampler Method Editor now contains an “Enable Barcode Reading” check
box. Selecting this check box (flag ON) will activate the barcode reading/storing feature. Clearing
this check box will disable barcode reading.
Figure 3-1
Enable Barcode Reading check box
Failed barcode readings
If a barcode reading is attempted but fails (due to torn, misplaced or missing labels and so on),
the barcode information for that particular sample will be displayed and stored as “N/A”.
Barcode reading disabled
If the user disables the barcode reading feature, no barcode information will be added to the data
file and results tables created from these files will not show a “Scanned Barcode’ column. If a
“mixed” group of samples (some with barcode information and others without) are used to create
a Results Table, the samples lacking barcode information will display “N/A” in the “Scanned
Barcode” column.
Backward and forward method compatibility
Methods created using the Analyst 1.6 software have not been fully tested with previous versions
of the Analyst software. All methods created with previous versions (1.5.x) can be used in the
Analyst 1.6 software.
The changes introduced in the Analyst 1.5.2 Software with HotFixes to February 2011 to the CTC
PAL Autosampler Method Editor are transparent to previous versions of the Analyst software.
That is, if an acquisition method is created with the Analyst 1.5.2 Software with HotFixes to
February 2011 and opened with a previous (supported) version of the Analyst software, the user
will not see the Enable Barcode Reading check box. Users will be able to modify, save, and use
these methods in previous (supported) versions of the Analyst software. Conversely, if users
create and save a CTC PAL method in a previous version of the Analyst software and open it in
the Analyst 1.5.2 Software with HotFixes to February 2011, they will see the Enable Barcode
Reading check box added to the method, defaulted to OFF. Users will then be able to enable
barcode reading, save the method, and use that method to scan and store barcode information.
Release Notes
RUO-IDV-03-0236-A
Analyst® 1.6.2 Software
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Notes on Use, Known Issues, and Limitations
Problem with multiple trays assignment
CTC Batch Editor Location tab sample assignments do not work properly if a tray position has
multiple trays assigned. Set the sample tray and vial positions from the Sample tab instead.
(SCR 12921, SCR 12923)
Message appears when uninstalling CTC cycle editor (v 2.0.7)
When uninstalling the CTC Cycle Editor, a message Remove Shared Files? appears. Click No. If
you click Yes, some required files installed by the Analyst software are removed, and the Analyst
software fails to activate the hardware profile that contains the CTC PAL autosampler.
Hardware profile must be reactivated to use the new custom cycles
Reactivate the hardware profile to view the new custom cycles created using the Cycle Editor.
(SCR 13501)
Injection valve switches when CTC method is aborted
The CTC injection valve switches after abort during injection. This can affect chromatography of
the subsequent analyses.
Terminal unlocks when CTC method is aborted
The CTC PAL terminal unlocks when the CTC method is aborted. To re-lock the CTC, reactivate
the hardware.
Network data folder
The CTC PAL data folder must be on a local drive. If it is on a network drive, the hardware profile
does not activate. (SCR 11665)
Shimadzu Devices
Layout of the 1.5 mL Cooled rack has been changed
A new High Capacity 1.5 mL Cooled rack has been introduced for the Shimadzu LC 30 series
autosampler. The layout has been changed to accommodate the 105 vials and therefore cannot
be selected using the existing 1.5 mL Cooled rack option from the Location tab in the Batch
Editor. To use this new rack, select the 1.5 mL Standard rack. The new rack will still be cooled.
(ST 34061)
IP address must be entered manually to establish an Ethernet connection
For Windows 7 users, when establishing an Ethernet connection, the Shimadzu device search
function cannot retrieve the IP address from the Shimadzu CBM. Users must manually enter the
IP address. (ST 29400)
If a different user logs on to the Analyst software, the Shimadzu AAO may stop
responding
In Mixed Mode, if a different user logs on to the Analyst software, the Shimadzu AAO may stop
responding. If this issue occurs, stop the AnalystService.exe and the ShimadzuAAO.exe using
Task Manager and then start the Analyst software. (ST 33331)
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Notes on Use, Known Issues, and Limitations
Batches can fail if post treatment cycle does not complete before sample
acquisition has completed
For the Shimadzu LC 30 series autosampler, when creating an acquisition method, do not select
After Acquisition from the Rinsing Start Time list on the Internal Rinse dialog. Select Specify Start
Time or do not use this option in the acquisition method. The internal rinse must be completed
before the sample acquisition has completed. (ST 33825)
Loss of queue functionality
Performing an abort when a Shimadzu device is in the Equilibrate mode (by manually putting the
device in the Standby or Ready mode before Equilibration has completed) results in a loss of
queue functionality. To regain control of the queue, stop the AnalystService and power-cycle the
Shimadzu stack. (SCR 9588)
No forward compatibility of Shimadzu hardware profiles created before Analyst®
1.4.2 HotFixes to November 2006
All profiles containing Shimadzu devices created before Analyst 1.4.2 HotFixes to November
2006 need to be recreated. However, all previously created methods will work with re-created
hardware profiles.
Shimadzu SIL-10AF and SIL-10Axl autosamplers are not supported
The Shimadzu SIL-10AF and SIL-10Axl autosamplers are not supported even though the option
exists in the Analyst software hardware configuration editor. Do not select these autosamplers as
you may not be able to activate the hardware profile.
Enabling additional devices in the Shimadzu Prominence stack
When additional devices are enabled in the Shimadzu Prominence stack (such as the Rack
Changer), a full reboot of the stack may be required to make sure that a hardware profile can be
successfully activated in the Analyst software.
Loss of synchronization when specifying short acquisition times with Shimadzu
Prominence stack
A loss of synchronization between the Analyst software and the Shimadzu Prominence stack
may occur if the acquisition time specified is shorter than the time necessary for the autosampler
to complete its rinse washes. Make sure your Mass Spec acquisition method is at least 1 to 2
minutes long.
Pump pressure maximum limit may need to be increased when creating Shimadzu
methods
The default pump pressure maximum limit may be too low and lead to pressure errors on the
hardware and subsequent acquisition errors. Therefore, the default limit may need to be
increased when creating Shimadzu methods.
No error message when missing Shimadzu deep-well plate
If a deep-well plate is missing in the Shimadzu autosampler, the autosampler fails to detect it and
the run proceeds without the software being notified of any error.
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Notes on Use, Known Issues, and Limitations
Issue when restarting AnalystService
If you reboot the computer or restart the AnalystService.exe (through the Windows Services
screen), the system may stop responding. Power cycle the Shimadzu controller and then activate
the hardware profile in the Analyst software to help restore the system. (SCR 13266)
Need Windows local administrator rights to modify hardware profile
To create or modify hardware profiles that include Shimadzu devices, you must be a Windows
Local Administrator or have equivalent permissions. When the Analyst software is installed,
previously existing Shimadzu profiles will not be usable until a Windows Local Administrator
activates the profile. (SCR 11858, SCR 13261)
Wrong vial number
When you use Shimadzu devices, the wrong vial number is sent to the autosampler when rack
type 4 is in use. (SCR 12010)
Reset the device from the controller manually
Reset the Shimadzu autosampler from the controller after an abort or failure. Currently, there is
no way for the Analyst software to do this automatically. (SCR 10532, SCR 12921)
Loss of queue functionality
Performing an abort during Shimadzu Equilibrate results in a loss of queue functionality. To
regain control of the queue, stop the Analyst Service software. (SCR 9588)
Issues due to mismatch of duration time
The default duration for Shimadzu methods is 90 minutes. When tuning with a mass
spectrometer scan duration shorter than the Shimadzu time program duration (as in the default
tune method), you will not be able to stop the tune run using the Analyst software once the mass
spectrometer has finished scanning. Press Run on the controller to stop the run or change the
default Shimadzu run duration to match the MS duration in the Shimadzu method editor. (SCR
9515)
Clearing “Fail whole batch in case of missing vial” does not work
Clearing this feature as found in Tools > Settings > Queue Options does not work. The batch fails
regardless of whether the user has selected this check box.
Shimadzu Rack Changer racks are incorrectly labeled
Currently, the Shimadzu Rack Changer racks are labeled as follows: 1.5 mL Vial Cooled, MTP 96
Cooled, MTP 384 Cooled, Deep Well MTP 96 Cooled, and Deep Well MTP 384 Cooled. The
Shimadzu Rack Changer racks are not offered in the cooled format but are incorrectly labeled
with the “Cooled” suffix. Ignore the “Cooled” suffix; these trays do not provide the cooling
capability. (ST 18032)
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Notes on Use, Known Issues, and Limitations
LC Packings Devices
Problem locating reagent vial positions
Famos Autosampler User Defined Program (UDP) does not properly locate Reagent Vial
positions. (SCR 12204)
Define pressure in bar units
When using the UltiMate Integrated System, select the pressures in bar units. (SCR 9257, SCR
13863)
Missing vials
Acquisition problems may occur if there are missing vials in a large batch with LC Packings
devices (both Famos and UltiMate). (SCR 9353)
DAD Devices
Single .wiff file for large data
Acquiring a large amount of data with a DAD (Diode Array Detector) device to a single .wiff file
may result in file corruption. To prevent this from happening, always acquire DAD data to multiple
.wiff files if you have a large number of samples.
Agilent Devices
All Agilent DAD should be <= 20Hz
Previously, it was recommended to acquire DAD data at acquisition rates of 40Hz and below.
With the Analyst 1.6.1 software, this guidance was lowered to 20Hz and below. Using higher
acquisition rates will cause the acquisition to take much longer than expected. The same
guidance applies to the Analyst 1.6.1 software. (ST 25396, ST 35524)
The Agilent 1260 DAD G4220B is not supported (ST 33318)
Agilent 1260 and 1290 pumps
The Agilent 1260 and 1290 pumps cannot be used in the same hardware profile. (ST 33313)
Agilent 1260 G1329B configuration
The Agilent 1260 G1329B autosampler must be configured as an Agilent 1200 G1329A
autosampler to operate. (ST 34104)
Compatibility with Agilent 1200 Methods
Acquisition methods that were created for Agilent 1200-series devices can be opened and used if
the current hardware profile includes Agilent 1260-series devices that are functionally equivalent
to the 1200-series device(s) used in the method. The following devices are functionally
equivalent:
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Notes on Use, Known Issues, and Limitations
•
1200 G1312B Binary Pump SL and 1260 G1312B Binary Pump
•
1200 G1316A Column Oven and 1260 G1316A Column Oven
Note: In order for methods to be compatible, all of the devices in the currently
active hardware profile must be the same as, or functionally equivalent to the
devices used in the original method.
Note: If a previously created (1200) acquisition method is used to acquire data
with a functionally equivalent 1260-series device, the File Information will show
that the acquisition method was created with a 1200-series device. To avoid this,
open the acquisition method with the new 1260-series device active in the
hardware profile and resave it (or save as a new method and use the new method
for acquisition).
Purging and Priming using the Analyst software
The 4220A Binary Pump now uses an integrated software-controlled purge valve. Previously,
users were responsible for manually purging and priming via a manual valve.
The Analyst software now supports this new functionality in both the Acquisition Method Editor
and Manual Tuning through a new Purge option.
Figure 3-2
New Purge option in the Acquisition Method editor
Figure 3-3
New Purge option in Manual Tuning
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Notes on Use, Known Issues, and Limitations
When the Purge option is activated, the Agilent 1290 Binary Pump will open the purge valve,
allowing system purging.
When creating a purging method, only the Total Time, Flow Rate and A/B(%) fields are used.
Anything entered into the Limits, Limits (Advanced) and Micro Mode tabs will be ignored.
Users can either use Manual Tuning to purge or prime their system, or they can create an
acquisition method that will be used exclusively for purging. This method can be submitted via
the Acquisition Batch Editor in the same manner as acquisition methods. Note that in this
scenario, the mass spectrometer will acquire data to the specified .wiff file.
Figure 3-4
Example acquisition batch with a purge method before acquisition
Changes to DAD acquisition
The Agilent 4212A and 4212B DADs have a single lamp source, rather than two lamps as in
previous DAD models. As a result, the usable wavelength range has been changed to 190–640
nm. Additionally, the 4212A DAD supports slit widths up to 8 nm, and the 4212B has a fixed slit
width of 4nm.
Baud Rate for Serial communication
If the Agilent 1290 or 1260 stack is configured for Serial (RS232) communication, ensure that the
baud rate is set in the Analyst software to 19 200.
Fractional injection volumes are not supported for Agilent autosamplers
When fractional injection volumes are requested, the decimal portion will be truncated and only
the integer value will be injected. For example, if an injection of 2.5 µL is attempted, the actual
injection will be 2 µL. (ST 28340)
Hardware profile containing an Agilent DAD 1315 D
When attempting to activate a hardware profile containing an Agilent DAD 1315 D that has an
incorrect IP address assigned to it, the Analyst software stops responding. Make sure that the
entered IP address is the actual address of the DAD.
Release Notes
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Notes on Use, Known Issues, and Limitations
Agilent wellplate
Agilent wellplate autosamplers generate a fault when a vial is missing. Reactivate the hardware
profile and device to recover. (SCR 12060)
Missing last decimal number in the status dialog
The flow rate of a PerkinElmer pump reported in the status dialog during acquisition is missing
the last decimal number. For example, if the pump flow rate is 0.075 ml/minute, the report shows
70 µl/minute instead of 75 µl/minute. (SCR 11370)
Agilent 1100 and 1200 peripheral devices cannot use CAN connections over
Ethernet
To use these peripheral devices, configure each peripheral independently using an Ethernet
connection through an Ethernet hub or connect each using an RS-232 cable. (ST 16108)
Tempo MDLC System
Acquisition with the Tempo™ MDLC system occasionally stalls
Occasionally, a sample in a batch submitted to the Queue shows as “acquiring” even after the
acquisition time is complete and the remaining samples show a status of “waiting”; the batch
never advances to the next sample. This issue is intermittent. If it occurs, resubmit the remaining
samples.
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4
21 CFR Part 11 Compliance
You can use the Analyst® 1.6.2 software to make sure that your site complies with the 21 CFR
Part 11 Electronic Records and Electronic Signatures regulations. This compliance relies on an
administrator’s ability to create a secure environment for generating, analyzing, and storing data.
Compliance often involves the software of many different vendors for functions ranging from
LIMS to data acquisition and from processing to archiving. The Analyst 1.6.2 software has the
necessary features for creating and maintaining an electronic record system by providing valid
electronic records of the acquisition and quantitative processing of data.
The Analyst 1.6.2 software is designed to be used as part of a 21 CFR Part 11 compliant system
and can be configured to support 21 CFR Part 11 compliance. Whether or not the usage of the
Analyst 1.6.2 software is 21 CFR Part 11 compliant is dependent on the actual usage and
configuration of the Analyst 1.6.2 software in the lab.
Validation services are available through AB SCIEX Global Services - Regulated and Clinical
Markets. For more information, contact softwarevalidation@absciex.com.
Release Notes
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21 CFR Part 11 Compliance
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Programs and Utilities
A
The following utilities are installed with the Analyst® software. They can be found in the \Program
Files\Analyst\Bin\ folder.
Table A-1
Utilities
Program
Description
Translat.exe
Utility to convert Agilent data files to the Analyst software data
format and Macintosh Library files to the Analyst software library
format. Enables creation of databases on SQL Server. Translat.exe
does not work over a network for Agilent data.
CFR_FileCheck.exe
Utility to rerun the installation qualification test. It is accessible from
the Windows Start menu.
Release Notes
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Programs and Utilities
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B
Technical Information Regarding Integration
Integration Issue Addressed in the Analyst® 1.4.2
Software
This issue is found using the manual-parameter portion of the IntelliQuan Algorithm (named
MQII). In the MQII portion of the IntelliQuan algorithm, a “Specify Parameters – MQII” mode
exists when the Show /Hide Parameters button is pressed twice. The issue has only been
observed when the “Specify Parameters — MQII” mode has been selected when reviewing the
results table and the associated peak review panes. The results were calculated independently
for the two displays and as a result conflicting data is observed.
The noise threshold calculation affects integration. During the process, the chromatogram is first
baseline-subtracted. The resulting chromatogram is then used to calculate the Noise Percent: a
method of setting the noise threshold by sorting all points by intensity, taking a point at the Noise
Percent percentile, and using its intensity level as a basis for the noise threshold.
Normally when the Noise Percent point falls on zero-signal sections of the baseline-subtracted
chromatogram, the noise threshold is calculated as zero and the noise percentage (Noise
Percent point) is automatically increased to more accurately reflect the noise in the baseline. This
results in the noise threshold recalculated to a more appropriate value and a lower peak area.
The issue occurs when the “Noise Percent” point falls on a point with a very small near zero
value, a numeric residual left after various numerical conversions and subtraction, that is usually
evaluated as zero. In this case, the noise percentage is calculated as a non zero number and is
therefore considered valid. The original noise threshold of approximately zero is chosen, instead
of increasing the Noise Percent point and recalculating the noise threshold. This results in a near
zero baseline and a slightly greater area under the peak being integrated.
The noise threshold value is lower than when the issue does not occur, leading to a higher
integration value.
Changes Introduced in the Analyst 1.5 Software
Scheduled MRM™ algorithm functionality has been added to the Analyst® 1.5 software. As part
of this functionality, the IntelliQuan integration mode has been adjusted for all integrations to
support unequal spacing of data points collected during acquisition. In addition, some smoothing
functionality has been updated in response to customer feedback. However, they do have a
minor affect on the way in which the area under the curve and peak height are calculated,
regardless as to whether the Scheduled MRM algorithm functionality is used.
These include:
•
Updating the IQA II and MQ III algorithms to use the trapezoidal area-under-thecurve method already used in the software with manual integration.
•
In the specific case of smoothing of data with a 5-point smooth or greater (7-point, 9point, for example), the interaction between the Savitsky-Golay smoothing algorithm
and the count values for the peak start and end has been adjusted to correctly
account for negative values created by the Savitsky-Golay smooth.
Release Notes
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Technical Information Regarding Integration
Guidance
•
For peaks with > 10 points across the peak, these updates will have minor effect,
most likely less than 1%.
•
For peaks with < 10 points across the peak, especially when put under a smooth of 5
points or more, the changes should result in a more accurate calculation of the peak
area, but the change will most likely be greater than 5%.
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