MassLynx 4.1 SCN 804 Release Notes SQ Detector 2

MassLynx 4.1 SCN 804 Release Notes SQ Detector 2
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MassLynx 4.1 SCN 804
Release Notes
SQ Detector 2
43464 Rev 01
Copyright © Waters Corporation 2011.
All rights reserved.
Copyright  2011 Waters Corporation
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Waters is a registered trademark, Waters the Science of What’s Possible and MassLynx are trademark of Waters Corporation
All other trademarks are the sole property of their respective owners
Table of Contents
MassLynx 4.1 SCN 804 .............................................................................................................. 3
Introduction ............................................................................................................................. 3
Applies to ............................................................................................................................. 3
Installation............................................................................................................................ 4
MS .......................................................................................................................................... 6
SQ Detector 2 ....................................................................................................................... 6
Adobe Print Driver Setup ........................................................................................................ 9
Inlets ................................................................................................................................. 10
Applications ........................................................................................................................... 11
MassLynx ............................................................................................................................ 11
Concessions ........................................................................................................................ 11
OpenLynx ........................................................................................................................... 11
Supported Computers, Operating systems, Hotfixes and Anti-Virus software .................................. 12
Antivirus ............................................................................................................................. 13
Windows Updates ................................................................................................................ 13
Uninstallation ...................................................................................................................... 13
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MassLynx 4.1 SCN 804
Introduction
The SQ Detector 2 is an advanced, small, robust and reliable single quadrupole mass detector for a
wide range of analytical and preparative chromatographic techniques. Designed and produced using
the principles of Waters’ Engineered Simplicity™ and combining the universal ionisation source and
IntelliStart™ technology with MassLynx™ informatics, the SQ Detector 2 guarantees maximum system
performance with minimum effort for set-up, sample runs and data interpretation.
Applies to
MassLynx 4.1 SCN 804 is a full install and applies to the following hardware configurations:
MS
Waters SQ Detector 2
LC
ACQUITY
ACQUITY
ACQUITY
ACQUITY
ACQUITY
ACQUITY
ACQUITY
ACQUITY
Binary Solvent Manager (ICS version 1.50.1521)
Sample Manager (ICS version 1.50.2736)
Sample Organizer
PDA Detector (ICS version 1.50.1121)
TUV Detector (ICS version 1.50.2530)
ELS Detector (ICS version 1.40.1882)
FLR Detector (ICS version 1.40.2407)
Column Manager (ICS version 1.50.1678)
ACQUITY
ACQUITY
ACQUITY
ACQUITY
UPLC H-Class and I-Class Systems
Sample Manager FTN (ICS version 1.50.1481)
Quaternary Solvent Manager (ICS version 1.50.1621)
Binary Solvent Manager (ICS version 1.50.1521)
Waters 2695 (controlled via IEEE)
Waters 2996 PDA
Operating Systems
Microsoft Windows 7 Professional 64 bit, Service Pack 1
Security
Basic and Full MassLynx security configurations are supported.
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Installation
MassLynx 4.1 SCN 804 is a complete installation of MassLynx 4.1. If MassLynx or any MassLynx SCNs
are already installed they must be uninstalled using Windows add/remove programs before installation
of MassLynx 4.1 SCN 804.
Please make sure that the “C:\Program Files (x86)\Micromass Utilities\ICOP” folder is deleted if
present after un-installation.
1. Close MassLynx and any other software applications.
2. If any instrument drivers - such as ACQUITY drivers, Waters 2777 / CTC drivers - have been
installed they must be removed using Windows Add/Remove programs before installing SCN
804.
3. If MassLynx (including V4.1) is installed, it should be removed using Windows Add/Remove
programs and the PC should be rebooted after the removal is complete.
4. Manually delete the "C:\Program Files (x86)\Micromass Utilities\ICOP" folder prior to
installation of SCN 804.
5. Install MassLynx V4.1 SCN 804 following the installation instructions starting at step 6 below.
6. Select Start–>Run from the windows start menu and type:
7. <DVD–Drive>:\setup
<return>
8. Where, <DVD–DRIVE> is the drive letter of the DVDROM.
9. Follow the instruction of the program.
10. Click Finish to complete installation of the SCN files.
11. Reboot the PC and log back into windows.
12. Reboot the instrument embedded PC.
13. Launch MassLynx.
14. Open Inlet Editor.
15. Install any required Waters instrument drivers (ICS) using the Deployment Manager by clicking
“Setup Instruments”. If any drivers are installed it is recommended that the PC is rebooted
afterwards before continuing the inlet system configuration.
16. Click “Configure” to launch the Inlet Configuration Dialog to complete the configuration of the
inlet system.
Note: Modifying or repairing an installation is not supported.
Note: OpenLynx must be installed if LCMS System Check is to be used. LCMS System Check can be
used with MassLynx Security.
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Installation of Stand–Alone Applications
This instruction is for installation of OALogin, OAToolkit, OpenLynx Browser and TargetLynx Browser.
If any of these applications are already installed they must be uninstalled using Windows add/remove
programs before installing the SCN 804 version.
1. Close any open software applications.
2. Insert the MassLynx SCN 804 DVD into the DVD–ROM drive.
3. Navigate to the Applications folder on the DVD and select the folder for the Application
required.
4. Run setup.exe
5. Follow the instruction of the program.
6. Click Finish to complete installation of the SCN 804 files.
Installation of Quanpedia databases
Example databases are available on a separate CD. These example databases should be copied onto
the PC and can then be opened in Quanpedia by selecting Options | Database | Open.
Files copied from a CD may have the read-only flag set and this will need to be removed.
To manually remove the read-only attribute from a file:
1. In Windows Explorer, right-click the file that you want to change, and then click Properties.
2. On the General tab, click to clear the Read Only check box.
3. Click OK.
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MS
SQ Detector 2
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Windows 7 with Service Pack 1 supported.
Secure install - Overwrite Raw Data permission is not required to generate IntelliStart Data.
The ASAP and APPI sources are supported.
Energy Saver mode.
SIR, 3ms minimum Dwell and 3ms inter-channel delay.
Automatic interscan tables are applied to all function switches involving an SIR function.
A "Low Flow Mode" option to shut off capillary / emitter voltage when waiting for inlet start has
been added.
Disabling of Corona current can be controlled via a method event.
MassLynx security timeout does not affect the creation and printing of IntelliStart reports. The
reports will be created and/or printed even if the MassLynx login window is present.
Concessions
General
• MassLynx will hang if user selects “Network” from the “Print Setup” dialog box. Printers must be
configured in the operating system first, as they will then be available in MassLynx “Print
Setup” without needing to click “Network”.
• Before importing existing projects into a secure install of MassLynx, the raw data files should be
removed from the project.
• Users must select an appropriate resolution reference file specific to their application.
• By design a non-admin user cannot adjust date and time settings.
• If there is arcing at the capillary tip users should manually lower the capillary voltage.
• Non OS Admin users cannot run ACQUITY Plot Viewer from C:\Program Files (x86)\Waters
Instruments\Bin folder.
• Shutdown tasks “Source Gas On” and “Source Gas Off” options are only present after starting
the Tune Page.
• To install ICS instruments older than 1.4 the ICSCompanionSetup.exe should be run manually.
• All EScI experiments should be run in the EScI ion mode, not the ESi Ion mode.
• All ASAP experiments should be run in the API ion mode.
• In dual polarity experiments, the experiment report readback section will show readbacks in the
polarity of the last active function.
• When running with a security enabled system you may be required to reboot the instrument PC
prior to opening MassLynx Security Manager. Upon opening MassLynx Security Manager you
may be warned that MassLynx applications are currently running. Reboot the windows PC to
enable access.
• Careful consideration should be given when setting up shut down methods. MS shutdown
actions should be placed after LC shutdown actions in MS error methods to ensure that LC
actions are able to complete even if MS communication is not available. LC shutdown actions
should be placed after MS shutdown actions in LC error methods to ensure that MS actions are
able to complete even if LC communication is not available.
• After linking a calibration to a tune file within the tune page the tune file must be saved before
the link is permanently stored.
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On rare occasions during the install, an error message is displayed stating that the DHCP
Server failed to register. If this message is seen, the installation should be cancelled and then
started again.
On rare occasions during an uninstall of MassLynx, an error message is displayed stating
“Waters DHCP error - 'Could not delete service'”. If this message is seen it should be
acknowledged and after the process has completed the PC should be rebooted before
attempting a further install.
The save option associated with a report produced by QC check does not work. As such, it is
not possible to rename the file and save elsewhere. Users need to record the file name and
generation time in order to return to it at a later date. Alternatively it can be printed upon
generation.
A Sample list batch can not be modified once it has been submitted.
Tune Page
• If there is a large difference in mass between one SIR trace and the next, a larger ICD/ISD may
be required if running with Manual Interscan delays.
Console / IntelliStart
• The console needs to finish loading before any options are selected. Closing the console before
this point can cause it to enter into an error state.
• When utilising IntelliStart, deleting the currently selected analysis from outside of the console
will cause the console to error.
• The resolution and calibration default Mass Range is restricted to 2 – 2048 Da, an increased
mass range can be set manually.
• The resolution and calibration default Mass Range is restricted to 2 – 2048 Da, an increased
mass range can be set manually.
• The advanced setup resolution and calibration Mass Range selected must encompass at least
four masses present in the selected reference file.
• Prior to running Intellistart calibration pre-check, it is advisable that the user check the signal
intensity of their masses of interest prior to running the check, ensuring that the correct cone
voltage is selected for the calibration compound in use
• Do not schedule an LCMS system check to run when another LCMS system check is going to
still be active.
• Manually changing the calibration file linked to a resolution file created via an IntelliStart
analysis will not be recognised by the IntelliStart system. Upon reselecting the analysis type via
the console, IntelliStart will continue to utilise the original linked calibration file.
• OpenLynx must be installed for the IntelliStart LCMS System Check feature to function.
• When using an LC system with IntelliStart, it is essential that the system is configured within
the Inlet Editor prior to the IntelliStart run. The IntelliStart system will fail to adjust the
desolvation temperature and gas flow if the LC system is not configured.
• For IntelliStart LC/MS System Check to be completed for both positive and negative ionisation
modes the individual analysis needs to be executed separately.
• The two ISD checks "LC/MS System Check Has Not Been Performed" and "LCMS System Check
Failure" have a higher priority than many of the other IntelliStart checks. In order to see these
other IntelliStart checks, the two higher priority checks can be disabled by de-selecting the
relevant option via the Configure > IntelliStart Configuration menu.
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MS Method - Alter existing file on disk
Instrument Resolution
Instrument Calibration
Sample Tune
Method Developer
System Check
Manual Optimization
MS Method - Create new file on disk
Required.
Required depending upon
actions
Acquisition - Start calibration acquisitions
Key
MS Calibration - Alter existing file on disk
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MS Calibration - Create new file on disk
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Tune Page - Alter tune file
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Tune Page - Create tune file
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Tune Page - Enter Autotune
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Tune Page - Enter System Console
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If an LC is not present in the system, the ISD checks relating to LC/MS, LC/MS System Check
Has Not Been Performed" and "LCMS System Check Failure", should be removed from the
system.
Entering the characters * / \ ? as part of names or filenames in IntelliStart will cause an error.
If the error is triggered click continue and rename the file using valid characters.
If the lamp parameter has been set to 'off' as a task during IntelliStart System Startup, the
instrument will also go out of operate when the lamp turns off.
When using the multiply charged function, within IntelliStart Develop Method, the mass to be
entered is the mass to charge ratio (m/z) of the precursor charge state of interest. The multiply
charged function will then complete the product ion scan to the mass range defined by the type
of analysis under investigation. If the mass range is not sufficient to observe the required mass
fragment, a new analysis type will be required with an appropriately calibrated mass range (up
to the limit of 2048m/z).
IntelliStart Sample Tune should only be run with a single polarity Ion Mode per sequence.
When running a Positive and negative Sample Tune Method Develop, only the most intense
peaks will be detected, not the most intense in each polarity. To get the most intense in each
polarity run the sequence in one ion mode and then the other appending the results to the first
existing method.
When rearranging instrument modules in the console the instrument image will show an
original SQD and not the new SQ Detector 2.
Manual optimisation should not be utilised when the ESCI+/- Source is selected.
When using IntelliStart in secure mode lock symbols on the IntelliStart main page indicate
additional user permissions are required to access the locked feature. The following permissions
are defined as required:
Tune Page – Enter tuning window
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To be able to run IntelliStart setup in Basic Security, users must have the ‘overwrite RAW
data’ permission enabled.
In Full Security regulated mode, HTML reports are now deleted following the completion of a
resolution setup and a sample tune develop method. In unregulated mode, the software
includes an option to retain the HTML reports.
Method Editor
• If an MS Method was created on a previous version of MassLynx, the user should open the file
in Method Editor and re-save the file before running on the instrument. This will ensure the
experiment's functions will be run in the order shown in Method Editor.
• We recommend the use of short scan times for both the ‘Switch From’ and ‘Switch To’ functions
when running Survey Functions. Use of long scan times reduces performance when switching
between functions.
• When setting up timed events involving fluidics care should be taken to ensure scheduled
events are giving enough time for each operation to complete. Attempting a fluidics timed
event while a previous fluidics timed event is still in operation may result in non execution of
the later event.
• When creating methods the following error message may be seen "The dwell times chosen
result in a cycle time below the recommended 80 milliseconds for ion mode switching. "Should
the dwell times be automatically updated?” Not selecting automatic update of dwell times may
result in a reduction of instrument lifetime.
• When creating method events, there should not be any events in between the solvent delay
start event and the solvent delay end event.
• Method Event initial settings should be used for events which are to occur at a time 0.0, if the
required event is not available in the initial settings it should be set to a time of 0.01.
Adobe Print Driver Setup
“Print to PDF” options in IntelliStart require the Adobe PDF print driver to be installed. This driver is
part of Adobe Acrobat Distiller, which is included in Adobe Acrobat Professional. The recommended and
validated version of Acrobat Professional to work alongside MassLynx is Adobe Acrobat Professional
9.0. Please install this version of Acrobat Professional before attempting to use MassLynx “Print to
PDF” options.
Software setup:
• Log in as an administrator and install ‘Adobe Acrobat 9’ using the default setup options. A
restart may be required.
• Once installation is complete, double click the 'Adobe Acrobat 9 Standard' link on your desktop.
• Read and accept the license agreement, then close the 'Adobe Acrobat' window.
The following steps apply to each user account on the host PC:
• View installed printers from the Windows Control Panel.
• Ensure 'Adobe PDF' is listed - do not alter its name.
• It is recommended that 'Adobe PDF' is not selected as the default printing device.
• Right click on 'Adobe PDF' and select 'Printing Preferences'.
• On the ‘Adobe PDF Settings’ tab, ensure the following options are selected:
o Default Settings: Standard
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Adobe PDF Security: as appropriate
Adobe PDF Output Folder: Prompt for PDF filename
Adobe PDF Page Size: as appropriate
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Ensure only the following boxes are checked:
o Rely on system fonts only; do not use document fonts
o Delete log files for successful jobs
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Press Apply and OK
Note: This configuration will allow the user to enable automated printing of PDFs in IntelliStart. To
configure PDF printing for OALogin, the 'Adobe PDF Output Folder' must be set to the OALogin
ReportDB directory (normally C:\MassLynx\OALogin\ReportDB).
To re-enable IntelliStart PDF printing, set the 'Adobe PDF Output Folder' back to 'Prompt for PDF
filename'.
Inlets
Concessions
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During inlet configuration, Waters deployment manager does not automatically launch when
required. Each ACQUITY component should be installed before configuring them in the inlet
editor using the "Setup Instrument" button in the inlet configuration window. A restart of the
host PC will be required after installation of the inlet driver.
Selecting “Cancel” from the Waters Pump Control method editor will cause a crash of the
method editor if running Waters Pump Control software 2.1 or higher
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If MassLynx is left in an error state for an extended period, the Solvent Monitor module may
crash.
There have been changes to the “ICOP” folder structure, The individual ICS installers are still
present, but whenever possible, ICS should be installed via the Deployment Manager (“Setup
Instrument” in Inlet Configuration Wizard).
It is recommended that users do not use a higher scan rate than 1 scan per sec with the
Waters 2996 detector.
When running ACQUTY Open Architecture System, the column temperature data channel should
be enabled in the ACQUITY Column Manager method.
The first time an ACQUITY system is initialized an error message about an ACQUITY server may
pop up. This can be safely ignored.
Applications
MassLynx
Concessions
•
Errors may be seen when running the Tools->Make Calibration process from the Spectrum
window, if this occurs run Process->Mass Measure before making the calibration.
OpenLynx
Concessions
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For UV data where part of the chromatogram trace is negative, OpenLynx Browser may
annotate some peaks with multiple peak descriptions. Multiple descriptions may be avoided by
setting the Chromatogram Peak Annotation Threshold to 1%.
The Acquity H-class / FTN plate display is not available in the Open Access Status Monitor.
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Supported Computers, Operating systems, Hotfixes
and Anti-Virus software
MassLynx 4.1 SCN 804 was tested and validated with Lenovo ThinkStation C20X workstations on:Microsoft Windows 7 Professional 64 Bit, Service Pack 1
The following Windows Updates are supported with MassLynx v4.1 SCN 804:
Update
Security
Security
Security
Security
Security
Security
Security
Security
Security
Security
Security
Update
Security
Security
Security
Security
Security
Security
Security
Security
Security
Security
Security
Security
Security
Update
Update
Security
Security
Security
Security
Security
Update
Security
Security
Security
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
Update
KB971033
KB2305420
KB2425227
KB2446710
KB2476490
KB2478662
KB2479943
KB2489256
KB2491683
KB2497640
KB2503658
KB2503665
KB2506014
KB2506212
KB2506223
KB2507618
KB2508272
KB2508429
KB2509553
KB2510531
KB2511455
KB2518869
KB2524375
KB2525694
KB2530548
KB2532531
KB2533552
KB2534366
KB2536275
KB2536276
KB2539635
KB2544521
KB2544893
KB2552343
KB2555917
KB2556532
KB2559049
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Security Update
Security Update
Security Update
Security Update
Update
Security Update
Update
Update
Service Pack
KB2560656
KB2562937
KB2563894
KB2567680
KB2570791
KB2570947
KB2616676
KB976902
KB976932
Antivirus
Symantec Endpoint Protection v11.0 anti-virus software is supported. It is recommended that
Network Threat Protection is disabled on the Acquisition PC.
Windows Updates
The PC firewall can occasionally be re-enabled by windows updates, after every update the firewall
should be checked to ensure it is still disabled.
Uninstallation
MassLynx can be removed by using the Windows ‘Add or Remove Programs’ facility in the Windows
Control Panel.
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