MassLynx 4.1 Getting Started Guide

MassLynx 4.1 Getting Started Guide
MassLynx 4.1
Getting Started Guide
71500113203/Revision A
Copyright © Waters Corporation 2005.
All rights reserved.
Copyright notice
© 2005 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF
AMERICA AND IRELAND. ALL RIGHTS RESERVED. THIS DOCUMENT
OR PARTS THEREOF MAY NOT BE REPRODUCED IN ANY FORM
WITHOUT THE WRITTEN PERMISSION OF THE PUBLISHER.
The information in this document is subject to change without notice and
should not be construed as a commitment by Waters Corporation. Waters
Corporation assumes no responsibility for any errors that may appear in this
document. This document is believed to be complete and accurate at the time
of publication. In no event shall Waters Corporation be liable for incidental or
consequential damages in connection with, or arising from, its use.
Waters Corporation
34 Maple Street
Milford, MA 01757
USA
Trademarks
Micromass and Waters are registered trademarks, MassLynx is a trademark
of Waters Corporation.
Other trademarks or registered trademarks are the sole property of their
respective owners.
Customer comments
Please contact us if you have questions, suggestions for improvements, or find
errors in this document. Your comments will help us improve the quality,
accuracy, and organization of our documentation.
You can reach us at tech_comm@waters.com.
Contacting Waters
You will be able to resolve most MassLynx issues yourself. However, if this is
not the case, you must contact Waters.
Customers in the USA and Canada should report maintenance problems they
cannot resolve to Waters Technical Service (800 252 4572). All others should
visit http://www.waters.com and click Offices, or phone their local Waters
subsidiary or Water corporate headquarters at 34 Maple Street, Milford, MA
01757, USA.
When contacting Waters, have the following information available:
•
The nature of the problem
•
Your instrument serial number(s)
•
Your software version (click Help > About in the main MassLynx
window)
•
Any error messages received
Table of Contents
Copyright notice ................................................................................................... ii
Trademarks ......................................................................................................... ii
Customer comments ........................................................................................... ii
Contacting Waters ............................................................................................. iii
1 Before you start ...................................................................................... 1-1
Introduction ....................................................................................................... 1-2
Installing MassLynx ......................................................................................... 1-4
Installing additional Application Managers................................................... 1-6
Preparing the system for use ......................................................................... 1-7
2 Starting MassLynx ................................................................................. 2-1
Opening MassLynx ........................................................................................... 2-2
The MassLynx window .................................................................................... 2-3
3 Creating a project .................................................................................. 3-1
Creating a new project .................................................................................... 3-2
Understanding project structure .................................................................. 3-4
4 Instrument setup .................................................................................... 4-1
Tuning your mass spectrometer .................................................................... 4-2
What is tuning?................................................................................................ 4-2
Tuning your instrument .................................................................................. 4-2
Mass calibrating your mass spectrometer .................................................. 4-5
What is mass calibration? ............................................................................... 4-5
Calibrating your instrument ........................................................................... 4-5
Setting up an inlet method ............................................................................. 4-6
What is an inlet method?................................................................................. 4-6
Choosing your pump, autosampler, and detector .......................................... 4-6
Table of Contents
v
Specifying your inlet settings.......................................................................... 4-7
5 Acquiring data ........................................................................................ 5-1
Acquiring data from the tune window ......................................................... 5-2
Acquiring data from the sample list .............................................................
Setting up an MS method................................................................................
Creating a Sample List....................................................................................
Starting data acquisition.................................................................................
5-3
5-3
5-4
5-9
6 Viewing, processing and storing results .......................................... 6-1
How to view, process, and store results ...................................................... 6-2
Viewing and manipulating chromatograms ............................................... 6-3
Opening the Chromatogram window.............................................................. 6-4
Using the Chromatogram................................................................................ 6-5
Displaying chromatograms ............................................................................. 6-7
Processing your chromatograms ................................................................... 6-10
Automating chromatogram display with Chrotool ...................................... 6-11
vi
Viewing and manipulating spectra ............................................................
Opening the Spectrum...................................................................................
Using the Spectrum .......................................................................................
Displaying spectra .........................................................................................
Processing your spectra .................................................................................
6-13
6-13
6-14
6-16
6-18
Processing and interpreting data ...............................................................
Quantitation using QuanLynx ......................................................................
Providing access and distributing results using OpenLynx ........................
Processing data using other Application Managers.....................................
6-21
6-21
6-21
6-22
Storing results in SDMS ................................................................................
Configuring MassLynx SDMS settings ........................................................
Sending data to SDMS ..................................................................................
Retrieving data from SDMS ..........................................................................
6-23
6-23
6-24
6-24
Table of Contents
A Additional OpenLynx installation instructions ............................ A-1
Installing OpenLynx Login .............................................................................
Sharing the installation directory on the MassLynx PC ...............................
Mapping a drive on the OpenLynx Login PC to the MassLynx PC ..............
Installing OpenLynx Login .............................................................................
A-2
A-2
A-3
A-3
Installing OpenLynx Toolkit .......................................................................... A-5
Typical hardware setup for OAToolkit ........................................................... A-6
Installing the software .................................................................................... A-6
Setting up the OAToolkit Service ................................................................... A-7
Remote Status Monitor.................................................................................. A-13
Installing Diversity browser ........................................................................ A-22
Index ..................................................................................................... Index-1
Table of Contents
vii
viii
Table of Contents
1
Before you start
This chapter will introduce MassLynx, explain installation, and describe
what you need to have ready before starting to use the software.
Contents:
Topic
Page
Introduction
1-2
Installing MassLynx
1-4
Preparing the system for use
1-7
1-1
Introduction
MassLynxTM is a powerful software application that configures and controls
your Waters mass spectrometer, and provides many features to analyze and
process the data acquired.
This guide will lead you through the steps you need to take to get started with
MassLynx and be quickly on the way to real, valuable results.
The following diagram shows the tasks that need to be performed to get up
and running with MassLynx; they will be outlined in more detail, step by step,
later in the guide.
1-2
Before you start
Steps to get started with MassLynx:
Prepare the
system for use
page 1-1
Start
MassLynx
page 2-1
Create a new
project
page 3-1
Setup your
instruments
page 4-1
Tuning
page 4-2
Calibration
page 4-5
Inlets
page 4-6
From the Tune
window
page 5-2
Using the
Sample List
page 5-3
Acquire data
page 5-1
MS Methods
page 5-3
View your data
page 6-2
Process your
data
page 6-21
Introduction
1-3
Installing MassLynx
In most cases MassLynx will be installed for you by a Waters engineer. If you
already have MassLynx installed, skip this section.
Requirements:
•
Before installing MassLynx, refer to the Release Notes for detailed
information relating to the release. You should also consult this
documentation if upgrading MassLynx, or if applying Software Change
notes (SCNs). If you are in any doubt about how to proceed, contact your
Waters support representative.
•
You may be asked for information about your mass spectrometer and PC
during installation. If you are unsure of any details, cancel the
installation wizard, confirm the information required, then begin the
installation procedure again.
•
You must be logged on to the PC using a user account that has
administrative privileges.
•
The PC you are installing MassLynx on must be running Windows XP
Professional SP2 or Windows 2000 SP4.
®
Prerequisites:
•
If you have previously installed Waters Instruments Component
Software, uninstall it using Windows Add or Remove Programs.
•
Close all running programs.
Installation tips:
•
QuanLynx, OpenLynx, and SDMS support are discussed in this
document. You may wish to review the information on those features
before deciding whether to install them. See Quantitation using
QuanLynx on page 6-21, Providing access and distributing results using
OpenLynx on page 6-21, and Storing results in SDMS on page 6-23 for
more information.
•
If you want to install OALogin, OAToolkit, or the Diversity browser,
refer to Additional OpenLynx installation instructions on page A-1.
To install MassLynx:
1.
1-4
If MassLynx has been supplied on a CD, or other removable media,
insert it into the appropriate drive.
Before you start
2.
After a few moments the installer should appear automatically. If it does
not, use Windows Explorer to navigate to the directory containing the
file setup.exe, and double-click the file; the MassLynx installer is
displayed.
3.
If the InstallShield Wizard informs you of required software to install
before the MassLynx can proceed (for example, JRE 1_5_0_3 and
Java3D 1_3_1), click Next to install it.
4.
Follow the on-screen instructions, choosing the features you wish to
install, referring to these guidelines:
•
Install MassLynx into the folder suggested – C:\MassLynx – and do
not move it after installation has completed.
Rule: Do not change the folder. MassLynx must reside on the C:
drive.
•
You will be given the option to install MassLynx with no security,
Basic Security, or Full Security. Many systems are installed with no
security, but if you need to restrict access to MassLynx or ensure
that files cannot be tampered with, select Basic or Full security. For
an explanation of these options, please see the MassLynx Security
Guide.
•
Key disks are required to install most Application Managers. You
will be asked to enter the location of the key disk during the
installation process. If you do not have an appropriate key disk –
and believe you should – contact your MassLynx system
administrator.
Tasks to complete after installing MassLynx:
1.
Remove the CD and store the key disks and the installation CD in a safe
place.
2.
Shut down the PC you have installed MassLynx on, restart it, and then
wait for the desktop to appear.
3.
Reboot your mass spectrometer’s embedded PC. For information on how
to do this, refer to the Operator’s Guide for your instrument.
4.
Wait at least 4 minutes before starting MassLynx.
Installing MassLynx
1-5
Installing additional Application Managers
Unless you have installed MassLynx with Full Security, it is possible to install
additional Application Managers at any time.
To install additional Application Managers:
1.
In Windows, open the Add or Remove Programs window from the
Control Panel.
2.
Click Micromass MassLynx V4.1.
3.
Click Change.
4.
Follow the on-screen instructions, selecting Modify – Add Application
Managers to existing MassLynx V4.1 Installation when that option is
presented.
Tip: If you want to install OALogin, OAToolkit, or the Diversity browser, refer
to Additional OpenLynx installation instructions on page A-1.
1-6
Before you start
Preparing the system for use
Before starting to use MassLynx to acquire and process data, you need to
make sure that your system is ready for use.
If you have an LC/MS system, it will contain some of the these components:
•
Pump (also known as a Solvent Delivery System). This will be a Liquid
Chromatograph (LC/HPLC/UPLC).
•
Autosampler.
•
Detector (usually PDA or UV).
•
Mass Spectrometer.
•
MassLynx PC.
Example LC/MS system layout:
Autosampler
Liquid
Chromatograph
Mass
Spectrometer
MassLynx PC
Preparing the system for use
1-7
If you have a GC/MS system, it will contain some of the these components:
•
Gas Chromatograph (GC).
•
Autosampler.
•
Mass Spectrometer.
•
MassLynx PC.
Before starting to use MassLynx, you will need to make sure that the
instruments are:
•
Properly installed
•
Properly connected
•
Switched on and ready
In many cases a Waters engineer will have installed and connected the
instruments for you. If you are not sure that the instruments are properly
installed and connected, refer to the instrument documentation or contact
your Waters support representative.
In addition to making sure that the instruments are ready, you should ensure
that the PC is turned on and that MassLynx has been successfully installed.
Once you have confirmed that the system is ready for use, move on to the next
section – Starting MassLynx.
1-8
Before you start
2
Starting MassLynx
This chapter will tell you how to open the MassLynx application and
explain the main features of the MassLynx window.
Contents
Topic
Page
Opening MassLynx
2-2
The MassLynx window
2-3
2-1
Opening MassLynx
To open MassLynx:
1.
Click Start > All Programs (or Programs) > MassLynx > MassLynx V4.1.
Alternative: Double-click the MassLynx V4.1 icon on the Desktop.
2.
If you have a security-enabled system, type your logon name and
password in the MassLynx Login dialog box. Check that the domain is
set correctly, then click OK.
Tip: If the MassLynx Login dialog box appears and you do not know a
logon name and password to access MassLynx, contact your MassLynx
System Administrator. If you have just installed a security-enabled
system and need assistance, refer to the MassLynx Security Guide.
2-2
Starting MassLynx
The MassLynx window
When MassLynx has opened you will see the main MassLynx window, similar
to the one shown below.
Typical MassLynx window:
Banner
Status bar
Menu bar
Tool bar
MassLynx bar
Sample List menu bar
Information bar
Sample List editor
The window contains:
•
A banner, which displays the names of the current project and Sample
List.
•
A top-level menu bar, providing access to some of the main features.
•
A tool bar, providing one-click access to different view modes and some
common features.
•
An information bar (below the tool bar), usually showing the status of
the sample currently being acquired or processed.
The MassLynx window
2-3
•
The MassLynx bar, with various tabs, at the left-hand-side of the
window. The contents of the MassLynx bar varies between Shortcut,
Queue and Status views, and as different tabs are selected.
•
The Sample List editor, where Sample Lists can be created, viewed and
edited.
•
A Sample List menu bar (above the Sample List editor), providing access
to commands associated with the Sample List.
•
A status bar, at the bottom of the window, giving information on
MassLynx’s current status.
The icons in the MassLynx bar provide access to most of the features available
in MassLynx, through a range of windows and dialog boxes. The tabs on the
left of the MassLynx bar control which icons are shown.
Example: To access instrument control features, click the Instrument tab on
the left of the MassLynx bar. The features available are shown in the
MassLynx bar, with an icon for each feature.
To open the Inlet Method editor, click Inlet Method (or the icon above the
text).
2-4
Starting MassLynx
3
Creating a project
Projects contain both the configuration files necessary to perform an
acquisition and the data that is acquired. This chapter will explain how
to create a project, and will describe the project structure so that you
find it easy to manage information later on.
Contents:
Topic
Page
Creating a new project
3-2
Understanding project structure
3-4
3-1
Creating a new project
A project contains the configuration information for your instruments and
stores the data that will be acquired. MassLynx will initially open with an
example project, but you should create your own project to store settings and
data.
Tip: Projects are flexible, and can hold a variety of settings that apply to a
range of requirements in one work area. Separate projects might be
appropriate for different work areas or users.
To create a new project:
1.
Click File > Project Wizard.
2.
Click Yes on the message warning that some services will be closed
down.
3.
In the Create Project dialog box, type a name for your project and,
optionally, a description.
4.
Enter the directory you want to create your project in.
Recommendation: Do not create projects in the directory in which
MassLynx was installed (usually C:\MassLynx) or any of its
subdirectories.
5.
Click Next, then select one of the three options for creating a project:
•
Create a completely new project
•
Create using current project as template – the method and
metadata files (such as tuning and calibration files) will be copied
into the new project. Select the box if you want to copy the sample
lists as well.
•
Create using existing project as template – the method and
metadata files (such as tuning and calibration files) will be copied
from the specified project into the new project created.
Tip: Unless you will be doing very similar work to someone who has
already been using the system, select Create new project.
6.
Click Finish.
Result: The new project has been created.
3-2
Creating a project
Take a few moments to read the next section, so that you can achieve your
goals more quickly by understanding projects.
Creating a new project
3-3
Understanding project structure
Understanding the structure of a MassLynx project helps you find the files
you need more quickly, and makes complicated tasks easier to perform. The
terms used might not be familiar at first, but you will come to understand
them as you work with MassLynx.
A directory, called <project name>.pro, will be created for each project. If a
new project is called MyProject, for example, a folder called MyProject.pro
would be created. Within this directory, a number of sub-directories are
created.
Project sub-directories:
Directory name
Contents
Acqudb
Acquisition information such as tuning parameters,
calibration settings, and inlet methods.
Curvedb
Quantitation calibration curve information.
Data
Raw data files.
Methdb
Method files for some Application Managers.
Peakdb
Peak list files.
Sampledb
Sample lists.
When data files are acquired they may contain more than one acquisition
function and may also contain processed data derived from the original raw
data – refined spectra, for example.
The data from each sample is placed into its own sub-directory within the data
directory. This sub-directory is called <file name>.raw, where the file name
has been specified by you – either in the Tune window or the sample list.
Details on the types of file created in these individual sub-directories can be
found in the MassLynx help.
3-4
Creating a project
4
Instrument setup
This chapter will outline the steps that need to be taken to set up your
system before data can be acquired.
Contents:
Topic
Page
Tuning your mass spectrometer
4-2
Mass calibrating your mass spectrometer
4-5
Setting up an inlet method
4-6
4-1
Tuning your mass spectrometer
What is tuning?
To obtain the most useful results from your mass spectrometry system, the
controls of the instrument need to be adjusted to achieve the best resolution
(narrowest peak) and highest sensitivity (tallest peak) possible.
You can make these adjustments through MassLynx and, on some
instruments, MassLynx can even tune the instrument automatically.
If the instrument is not tuned properly, the results you obtain will be less
useful, and possibly even misleading.
Tuning your instrument
The instrument is tuned from the Tune window. To open the Tune window,
click MS Tune on the MassLynx bar, Instrument tab; the Tune window for
your instrument will appear.
MassLynx is capable of controlling many different types of mass spectrometer,
so the exact display of the Tune window will vary substantially from
instrument to instrument. The Tune window for each instrument provides
access to instrument controls on the left hand side and a peak display on the
right hand side.
Warning: Consult the safety information in the Operator’s Guide for your
mass spectrometer before commencing the tuning process.
To tune the instrument:
1.
Supply a known sample to the mass spectrometer.
2.
Adjust the instrument controls to achieve the best peak shape possible.
3.
Save the tuning settings by clicking File > Save As in the tune window.
Detailed instructions on how to do this are supplied in the Operator’s Guide
for your mass spectrometer.
4-2
Instrument setup
The AutoTune Wizard
For ZQ, Quattro Micro API, and Quattro Premier instruments, the AutoTune
Wizard helps tune your instrument by automatically adjusting the instrument
controls until the best peak shape is achieved.
The AutoTune Wizard also provides the ability to automatically mass
calibrate the instrument, and to setup MS methods. Information on mass
calibration and setting up MS methods is given later in this document (see
Mass calibrating your mass spectrometer on page 4-5 and Setting up an MS
method on page 5-3).
Rule: AutoTune can only be used for samples that are supplied to the mass
spectrometer by infusion.
Recommendations:
•
AutoTune is only suitable if you have a small number of compounds to
tune.
•
It is recommended that a calibration (see Mass calibrating your mass
spectrometer on page 4-5) is performed at the same time as a full
Autotune.
To run the AutoTune Wizard:
1.
Infuse a suitable tuning and calibration solution to the instrument for
use during the process. The sample should be as pure as possible, and
you should know the masses of the compounds it contains.
If you are in doubt about how to infuse a sample, consult the Operator’s
Guide for your instrument.
2.
In the tune window, click Options > AutoTune; the AutoTune Wizard
appears.
3.
Select AutoTune - Full, and Calibrate Instrument.
4.
Click Next, then enter the file names you wish to use to save your tune
settings.
5.
Check that the temperatures to be used are appropriate.
Tip: The default temperatures are likely to be appropriate if you are
infusing the sample in combination with a mobile phase at high flow
rate.
Tuning your mass spectrometer
4-3
If you are infusing at a low flow rate, select the Adjust Default
Temperatures box. The temperatures that are then displayed (which can
be adjusted if required) are likely to be appropriate for low flow rate
infusions.
To revert to temperatures appropriate for a high flow rate, clear the
Adjust Default Temperatures box.
If you are in doubt, consult the Operator’s Guide for your instrument.
6.
Click Next, then enter an appropriate calibration reference file for the
sample you are infusing, and the file name you wish to use to save your
calibration settings.
7.
Check that the calibration range settings are appropriate – their default
values are likely to be sensible in most situations.
8.
Select whether a printed calibration report should be generated.
9.
Click Next, then enter the masses for the sample you are going to use
during the tuning process. You can choose to fill these values
automatically from the Tune window or calibration file, if required.
10. Set the Span for each mass to 5.
11. Check that the setting for desired peak width is appropriate: the default
values will be sensible in most situations.
12. Click Next.
Result: The AutoTune process will begin.
13. When you are shown the results at the end of the AutoTune, you can
choose to Finish and save the tuning and calibration settings, or to go
Back and repeat the process with different settings or a different
sample.
4-4
Instrument setup
Mass calibrating your mass spectrometer
What is mass calibration?
Once the best peak shape possible has been achieved through tuning, the
instrument needs to be calibrated so that the peak is recorded at the correct
mass.
MassLynx provides an automated method to do this. A reference file,
containing the expected masses of the peaks for a known sample, is compared
against the peaks obtained when an acquisition is performed on the known
sample.
At the end of the process, the instrument will be calibrated to provide accurate
results. You must re-calibrate the instrument from time to time, as detailed in
the Operator’s Guide for your mass spectrometer.
Calibrating your instrument
The particular method of calibration will vary between instruments, but it is
normally performed through the calibration window. To open the calibration
window, click MS Tune on the Instrument tab of the MassLynx bar, then click
Calibration > Calibrate Instrument.
Detailed instructions on how perform calibration are supplied in the
Operator’s Guide for your mass spectrometer.
The AutoTune Wizard
If you have a ZQ, Quattro Micro API, or Quattro Premier instrument, you can
calibrate using the AutoTune Wizard. For details on how to do this, see The
AutoTune Wizard on page 4-3.
ToF calibration
For some time-of-flight (ToF) and quadropole time-of-flight (Q-ToF)
instruments, a wizard is provided to help you calibrate the instrument. The
wizard assists you in preparing the mass spectrometer for the acquisition of
accurate mass data.
For details on calibrating your ToF instrument, refer to the online Help for
your instrument.
Mass calibrating your mass spectrometer
4-5
Setting up an inlet method
What is an inlet method?
Mass spectrometers are often used in conjunction with an inlet system such as
a liquid chromatograph (LC) or a gas chromatograph (GC). MassLynx can
control this equipment during data acquisition to provide complete control of
an experiment. Autosamplers will often be used to automate the running of
samples.
An inlet method is a group of settings for the inlet system. An inlet method
can be created and then specified for use during an experiment, and those
settings will be applied during the data acquisition. A number of different
inlet methods can be created, saved, and used for different types of
experiment.
Choosing your pump, autosampler, and detector
Inlets are configured through the Inlet Method window. To open this window,
click Inlet Method on the MassLynx bar, Instrument tab; the Inlet Method
window will appear.
To select the inlet modules you are using:
1.
Click Tools > Instrument Configuration; the Inlet Configuration dialog
box is displayed.
2.
Click Configure; the Inlet Configuration Wizard is displayed.
3.
Select the required pump (often a liquid chromatograph or gas
chromatograph), and click Next.
4.
Select the required autosampler, and click Next.
Restriction: Only the autosamplers that are compatible with the chosen
pump will be displayed.
5.
Select the required detector, and click Next.
Restriction: Only the detectors that are compatible with the chosen
pump and autosampler will be displayed.
4-6
Instrument setup
6.
Depending on the configuration selected, the HPIB Communication or
GPIB Communication settings may be displayed. If they are, enter
appropriate values and click Next.
7.
The Configuration Successful message is displayed. Click Finish to
return to the Inlet Configuration dialog box, then Finish again to return
to the main Inlet Method window.
Depending on the inlet modules selected, installation wizards may appear to
guide you through the installation of specific software relating to those
modules. If so, follow the on-screen instructions, selecting the options
appropriate for your system.
Specifying your inlet settings
The configuration options available vary substantially between different
inlets. In all cases, however, you access the options by clicking the icons in the
Inlet Method window bar on the left side of the screen.
In the Inlet Method window bar there will be a Status icon – providing access
to information on the current inlet status – and one or more of the following
icons, depending on the inlet equipment you have specified:
•
Inlet
•
Autosampler
•
Detector
You can also specify the way in which inlet or detector runs should be
triggered, that data acquisition should only commence when certain events
are detected, and that events should be sent to the inlet system at the end of
acquisition. These features are configured using the Events and Triggering
Wizard, accessed from the Inlet Configuration dialog box.
Detailed instructions on how to configure the options available for your inlet
are available by clicking Help > Help On Inlet, Help > Help On AutoSampler,
and Help > Help On Detector, respectively. Help for the Inlet Method window,
including how to use the wizards, is available by clicking Help > Help On
Editor.
Recommendation: To obtain the best results, refer to the documentation
supplied with your inlet equipment as well as the MassLynx documentation.
Setting up an inlet method
4-7
4-8
Instrument setup
5
Acquiring data
This chapter will explain how you acquire data using MassLynx. It will
cover how to:
•
Acquire data for a single sample through the Tune window.
•
Create MS methods and Sample Lists for automated data
acquisition.
Contents:
Topic
Page
Acquiring data from the tune window
5-2
Acquiring data from the sample list
5-3
5-1
Acquiring data from the tune window
The easiest way to acquire data is directly from the Tune window. When using
this method you can:
•
Start and stop acquisitions
•
Control most of the scanning parameters
The disadvantages of this method are that you cannot:
•
Use inlet methods
•
Acquire SIR (Selected Ion Recording) or MRM (Multiple Reaction
Monitoring) data
•
Acquire analog data
•
Acquire data from multiple samples unattended
If you need to use any of these features, acquire data using the Sample List.
To acquire data from the Tune window:
1.
Click MS Tune on the Instrument tab of the MassLynx bar to open the
Tune window.
2.
Ensure the instrument is in Operate mode. If the indicator in the bottom
right of the Tune window is not green, click the adjacent Operate button.
3.
Click the Acquire button; the Acquisition Setup dialog box is displayed.
4.
Enter the settings you wish to use for the acquisition.
5.
Click Start.
Caution: MS instruments require the Tune window to be open to acquire data,
whether the acquisition is done directly from the Tune window or by using the
Sample List. If you try to close the Tune window, a warning message will be
displayed to this effect; if you choose to close the window anyway then
acquisition will stop.
5-2
Acquiring data
Acquiring data from the sample list
Setting up an MS method
What is an MS method?
Mass spectrometers can acquire a number of different types of data from the
samples supplied. While these will vary depending of the capabilities of the
instrument they may include, for example:
•
a scan over a specified range of masses
•
a scan of a single targeted mass
•
the results of scanning the fragments of particular target ions
Different data types can be acquired from a sample in a single experiment.
An MS method is a group of settings defining the scans that the mass
spectrometer should perform. Once an MS method has been saved, these
settings can used when acquiring data from samples.
Setting up MS methods
Detailed instructions on the options available when setting up MS methods
are supplied in the Operator’s Guide for your instrument. If you have a ZQ,
Quattro Micro API, or Quattro Premier instrument, you may be able to set up
SIR and MRM methods using the AutoTune wizard – refer to the online Help
supplied with the instrument for more information.
MS methods are set up using the Experiment Setup window. To open this
window, click MS Method on the Instrument tab of the MassLynx bar.
The window contains the current list of functions – types of scan – that have
been defined for the MS method. The buttons on the tool bar indicate the
different types of function available for your instrument. Click these buttons
to add a function of that type to the MS method.
To the right of the description for each function is a colored bar showing the
time period over which the function will be used. The total time for the MS
method is displayed between the tool bar and the function list: this can be
modified by typing a new value in the Total Run Time box.
Acquiring data from the sample list
5-3
Save the MS method when you have finished setting it up, so that it can be
used when data is acquired.
Tip: Unless you wish to overwrite the existing MS method, save the file with a
new name.
Creating a Sample List
What is a Sample List?
A MassLynx Sample List is a list of the samples available for analysis by the
mass spectrometer. Among other things, it can include:
•
Information on the name to be given to the data acquired
•
Inlet methods to use
•
MS methods to use
•
Tune settings to apply
A Sample List can be set up for each different set of samples you wish to run,
then saved and loaded as it is needed. You can create as many Sample Lists as
you like for each project. The Sample List that was open last will be
automatically loaded when MassLynx starts.
Sample Lists are also utilized by the Application Managers – such as
QuanLynx – that can be used to process your data.
Tips:
5-4
•
The Sample List display can be customized to hide some of the columns
shown by default, and to add many more. Choosing the right columns for
the work you are doing can help improve your efficiency when working
with MassLynx. For more details, see Customizing the Sample List
display on page 5-8.
•
Information in hidden columns can influence the way the system
operates. If you experience unexpected behavior when running a sample
list you have not created yourself, temporarily display the hidden
columns to check the contents. For more details, see Customizing the
Sample List display on page 5-8.
Acquiring data
Minimum requirements for the Sample List
If there is an inlet connected, your sample list must contain – as a minimum –
the columns indicated in the table below.
Required sample list columns:
Column name
Field ID
File Name
FILE_NAME
Inlet File
INLET_FILE
MS File
MS_FILE
Bottle
SAMPLE_LOCATION
Inject Volume
INJ_VOL
Tip: As column names are configurable, they may differ from those given
above. The field IDs will remain the same whatever the name of the column.
With these columns displayed, the Sample List will look similar to this:
Example Sample List:
Using a sample list with these columns will enable you to acquire a basic raw
data file. When using an Application Manager to process data, more columns
will normally be required – refer to the Application Manager’s help for details.
Creating or editing a Sample List
The Sample List, displayed in the main MassLynx window, is similar to a
spreadsheet. You can type values directly into the highlighted cell or,
depending on the type, right-click or double-click in a cell to choose a file or
from a list of options. You can also copy, cut, and paste cells, rows, and
columns.
To add another sample (row):
1.
On the Sample List menu bar, click Samples > Add.
2.
Enter the number of samples you wish to add.
Acquiring data from the sample list
5-5
3.
Click OK; the new samples will be added to the bottom of the Sample
List.
You can also insert rows for additional samples by clicking Samples > Insert;
the new sample row is inserted above the current selection.
Filling cells automatically
Rather than entering values individually into every cell in the Sample List, it
is possible to automatically fill cells, saving on time and replicated effort.
There are a number of different features available to help you:
Adding new sample rows
When you add or insert new rows, the values from the row above are
automatically inserted into the new row.
Entering appropriate values for one row and then creating a
number of new rows is much quicker than creating empty rows first
and then entering appropriate values manually.
Fill down
The fill down feature enables the contents of one cell to be inserted
into multiple cells on subsequent rows.
To use this feature, select an area more than one row in depth and,
on the Sample List menu bar, click Samples > Fill > Down. The
contents of the first selected cells will be inserted into the cells
below.
Fill series
The fill series feature will insert the contents of one cell into
multiple cells on subsequent rows, incrementing the numerical
values for each cell. If the first cell contains 1:20, for example, the
next cell would have 1:21 inserted, the next 1:22, and so on.
To use this feature, select an area more than one row in depth and,
on the Sample List menu bar, click Samples > Fill > Series.
The autosampler bed layout
If you have a Waters or Gilson autosampler installed, you can use
the autosampler bed layout display to insert information directly
into the Sample List.
5-6
Acquiring data
To insert information from the autosampler bed layout:
1.
Click Samples > AutoSampler Bed Layout.
Result: The AutoSampler Bed Layout dialog box is displayed.
2.
Select the samples you wish to add to the Sample List.
3.
Use the buttons at the top of the dialog to add samples to the list,
replace the selected sample, or insert the sample at the selected line.
More than one sample can be added at once.
Copying data from a spreadsheet
Spreadsheets created in other Windows applications can be copied
into the Sample List.
To copy data from a spreadsheet:
1.
Add rows and columns to the Sample List so that it matches the
number of rows and columns in the data you want to copy.
2.
Select the relevant area in the other Windows application, then copy
it.
3.
Click Edit > Paste on the Sample List menu bar.
Caution: Data will be lost if the Sample List does not have the same
rows and columns as the spreadsheet information being copied.
Specifying the inlet and MS method
If you have worked through What is an inlet method? on page 4-6 and Setting
up MS methods on page 5-3, one or more inlet method and MS method files
will have been created. These files will be used during data acquisition.
To specify which inlet method to use:
1.
Double-click in the Inlet File column for the sample.
Alternative: In the Inlet File column for the sample, right-click, then
click Browse.
2.
Click the inlet method you want to use; click OK.
Acquiring data from the sample list
5-7
To specify with MS method to use:
1.
Double-click in the MS File column for the sample.
Alternative: In the MS File column for the sample, right-click, then click
Browse.
2.
Click the MS method file you want to use; click Open.
Tip: If you cannot see these columns, customize the display so that they are
visible. See Customizing the Sample List display on page 5-8 for details.
Importing Sample Lists and data
MassLynx allows you to import complete Sample Lists from other software
applications, and also provides a feature for you to import data into Sample
Lists you have created. OpenLynx batch files, (*.olb) containing lists of
samples that failed to run, can also be imported directly into the Sample List.
For detailed information on how to import Sample Lists and data, refer to the
main online MassLynx Help.
Customizing the Sample List display
Many different columns of information can be displayed in the Sample List.
The display you choose will be saved when you save the Sample List, although
the display format can also be saved separately if you wish.
Tip: Displaying the most appropriate columns, and hiding those that are not
needed, will help you to quickly see everything you need without being
distracted by unnecessary information.
To customize visible columns and column order:
1.
On the Sample List menu bar, click Samples > Format > Customize.
Alternative: Right-click on the Sample List and click Customize Display.
5-8
2.
In the Customize Field Display dialog box, select the boxes next to
columns you want to be visible, and clear the boxes next to columns you
want to hide.
3.
To change the order of columns, select a column in the list and click the
Move up or down arrows until the column is in the required position.
Repeat this for other columns if necessary.
4.
When you have finished making changes, click OK.
Acquiring data
To customize column titles, decimal places, and alignment:
1.
Click a cell in the column you want to modify, then – on the Sample List
menu bar – click Samples > Column > Properties.
Alternative: Right-click on the column heading and click Properties.
2.
Modify the column title, alignment, and (for numeric columns only) the
number of decimal places displayed.
3.
Click OK.
Starting data acquisition
The process of acquiring data is simple and straightforward: all the work you
have already done in tuning and calibrating the instrument, and configuring
the inlet and MS methods, is utilized at this stage.
To start data acquisition:
1.
Click MS Tune on the Instrument tab of the MassLynx bar to open the
Tune window.
Caution: MS instruments require the Tune window to be open to acquire
data, whether the acquisition is done directly from the Tune window or
by using the Sample List. If you try to close the Tune window a warning
message will be displayed to this effect: if you choose to close the window
anyway then acquisition will not proceed.
2.
Ensure the instrument is in Operate mode. If the indicator in the bottom
right of the Tune window is not green, click the adjacent Operate button.
Tip: Instruments must be in Operate mode to acquire data. The current
status of the instrument can be checked either in the Tune window – the
indicator at the bottom right of the window will be colored green if the
instrument is in Operate – or by clicking the Status button on the
MassLynx tool bar.
3.
In the main MassLynx window, click
.
Alternative: Click Run > Start.
Result: The Start Sample List Run dialog box is displayed.
Acquiring data from the sample list
5-9
Start Sample List Run dialog box:
4.
Make sure that the Acquire Sample Data box is selected, and that the
samples to be run are correctly indicated. The other options (to perform
Pre-Run and Post-Run processes, and to Auto Process Samples) should
be left unselected unless you know that you want to perform these
actions.
5.
Click OK.
Result: MassLynx checks the Sample List to validate the entries and
methods specified, then begins data acquisition. If any problems are
found, explanatory messages will be displayed, and acquisition will not
begin.
Tip: If data acquisition does not begin, check that the inlet is connected
and not in error, and that you have not accidentally clicked the Pause
button on the MassLynx tool bar.
Viewing the data acquisition progress
During acquisition, the Information bar above the Sample List will provide
information on the progress of the acquisition. You can see all the jobs
currently running, waiting, or paused by clicking the Queue button on the
MassLynx tool bar. The status of individual jobs can then be viewed by
clicking on the job in the MassLynx bar.
5-10
Acquiring data
Viewing the chromatogram and spectrum during data acquisition
To view the chromatogram for the data currently being acquired:
1.
On the Sample List menu bar, click Chromatogram to open the
Chromatogram window.
2.
Click
. The chromatogram display is updated as the acquisition
proceeds.
Alternative: Click Display > Real-Time Update.
To view the spectrum for the data currently being acquired:
1.
On the Sample List menu bar, click Spectrum to open the Spectrum
window.
2.
Click Display > Real-Time Update; the Spectrum Real-Time Update
dialog box is displayed.
3.
Select Enable Real-Time Update.
4.
Select the type of data you want to display; click OK.
Acquiring data from the sample list
5-11
5-12
Acquiring data
6
Viewing, processing and storing
results
This chapter will explain how you can:
•
View the data you have acquired
•
Manipulate the display to get the most useful results
•
Move on to more advanced processing of your data
•
Store your results
Contents:
Topic
Page
How to view, process, and store results
6-2
Viewing and manipulating chromatograms
6-3
Viewing and manipulating spectra
6-13
Processing and interpreting data
6-21
Storing results in SDMS
6-23
6-1
How to view, process, and store results
Acquiring data by running samples is usually just the beginning – you want to
view the results obtained, store them for future reference, and, perhaps,
process them to gain further understanding or enhance clarity.
The steps that need to be taken will depend on what you are trying to achieve
with your work. MassLynx and the Application Managers provide a great
many options to help you, but it is usual to begin by viewing the
chromatograms and spectra obtained from the samples.
You can concentrate on certain parts of the chromatogram or spectra, and
manipulate them to improve the clarity of the results – to remove background
noise, for example. You can also display spectra related to specific
chromatogram points, and the chromatograms associated with individual
spectra.
You can then process the results by using the Application Managers included
with MassLynx (QuanLynx and OpenLynx) to gain more value from the data
acquired, and access other optional Application Managers that provide
features specific to the type of work being done.
The results will be saved within the project you created. If you have Waters
NuGenesis SDMS (Scientific Data Management System), the results can be
stored there for sharing and review across your enterprise.
6-2
Viewing, processing and storing results
Viewing and manipulating chromatograms
There are a number of different types of chromatogram that can be displayed
by MassLynx. It is helpful to have a concept of what each one means so that
you can choose the most appropriate type for your needs.
Types of chromatogram:
Chromatogram type
Description
Total Ion Current
(TIC)
Usually the default type of chromatogram opened in
MassLynx, a TIC chromatogram can be thought of
as a summed spectrum plotted over time. It shows
the total current resulting from the detection of ions
(of whatever mass) over the period of the MS scan.
Base Peak Intensity
(BPI)
A BPI chromatogram is a variant of a TIC
chromatogram. It plots, for each scan throughout the
period of the MS scan, the intensity of only the most
abundant ion at the time of that scan. It ignores all
the other, less abundant, ions detected at the same
time.
The BPI chromatogram exhibits a greater apparent
resolution and signal-to-noise but will only contain
contributions from the most intense components.
Therefore, it is possible that some peaks in the TIC
chromatogram may not be visible in the BPI
chromatogram.
Mass
A mass chromatogram shows the ion current
resulting from a specified mass only.
The mass chromatogram can reduce complexity and
make it easier to identify a known component.
Analog
During an acquisition, MassLynx can store analog
information obtained from an auxiliary source such
as a UV detector. If analog data has been acquired it
can be displayed using an analog chromatogram.
Viewing and manipulating chromatograms
6-3
Opening the Chromatogram window
Chromatograms acquired in your data files are viewed using the
Chromatogram window.
To open the Chromatogram window:
1.
In the Sample List, click the number to the left of the sample you wish to
view, so that the whole row is highlighted. You can choose more than one
sample by clicking to the left of the first sample and dragging to the last.
2.
On the Sample List menu bar, click Chromatogram.
You will now see the chromatogram of the data acquired from running the
selected sample. Time is shown along the x axis (horizontal) and intensity is
shown along the y axis (vertical).
There are several important areas on the screen to note:
Typical Chromatogram window:
Data file name
Active trace indicator
6-4
Viewing, processing and storing results
Function (type of scan)
Type of chromatogram
Number of ions detected at
the largest peak
Tips:
•
The information displayed in the Chromatogram window can be
configured by clicking Display > View > Header. For information on how
to use this feature, refer to the MassLynx Help.
•
You can also open the chromatogram for a data file from the Spectrum
window. For details, see Using the Spectrum on page 6-14.
Using the Chromatogram
To focus on the most important areas of the results, the Chromatogram
display can be changed in a number of ways. Some of the most commonly used
are:
•
Showing only part of the chromatogram
•
Magnifying the chromatogram, or part of the chromatogram
•
Opening the spectrum relating to a point, or range, on the
chromatogram
Showing part of the chromatogram
To show part of the chromatogram:
1.
Click on the furthest left part of the chromatogram you wish to see.
2.
Drag to the furthest right part of the chromatogram you wish to see; a
line will be drawn to show how much of the chromatogram will be
displayed.
3.
Release the mouse button; the chromatogram display will be updated.
Alternatives:
•
Click Display > Range > From to set the beginning and end time values
manually.
•
Click Display > Range > Center > On time to center the display on a
specified time value.
To revert to seeing all of the chromatogram, click the
click Display > Range > Default, and click OK.
tool bar button, or
Viewing and manipulating chromatograms
6-5
Magnifying the chromatogram
To magnify the chromatogram:
1.
Activate the chromatogram you want to magnify by clicking on it; the
active trace indicator should appear beside it at the left of the window.
2.
Click the
tool bar button; the chromatogram trace will be magnified,
with the degree of magnification indicated at the top left of the trace.
3.
To magnify the chromatogram further, click the button again.
To reduce the degree of magnification, click the
tool bar button.
To magnify part of the chromatogram:
1.
Activate the chromatogram you want to magnify by clicking on it; the
active trace indicator should appear beside it at the left of the window.
2.
Click Display > Range > Magnify.
3.
In the Chromatogram Magnify dialog box, type a custom magnification
in the By box.
4.
In the From and To boxes, type the times to which you would like to
apply the magnification.
5.
To specify a different magnification for another time range, select
another number from the Range list, then repeat steps 3 and 4.
6.
Click OK.
To revert to seeing the chromatogram without magnification, click the
tool bar button.
Opening a spectrum from the chromatogram trace
Opening the spectrum for a single point on the chromatogram
To open the spectrum for a single point on a chromatogram trace, right-click
on the point of the chromatogram for which you want to see the spectrum. The
Spectrum window will appear, showing the relevant spectrum.
A ‘pointer’, made up of a triangle
and a line running through the
chromatogram trace, should appear at the point you clicked in the
Chromatogram window. If it does not, make it visible by clicking Display >
6-6
Viewing, processing and storing results
Pointer. You can display the spectrum for different points on the
chromatogram by dragging this pointer left and right along the trace.
You can open further spectra in the Spectrum window by right-clicking on
other points on the chromatogram trace.
Opening the spectrum for a chromatogram range
You can also display a combined spectrum relating to a range of points along a
chromatogram trace.
Tip: This feature is often used to produce a combined spectrum for a peak in
the chromatogram.
To display a combined spectrum for a chromatogram range:
1.
Right-click on the furthest left point you wish to include.
2.
Drag to the furthest right point you wish to include; a line will be drawn
to show how much of the chromatogram will be included.
3.
Release the mouse button; the Spectrum window will display the
combined spectrum.
Displaying chromatograms
You can display various types of chromatogram, as outlined in Viewing and
manipulating chromatograms on page 6-3, depending on the type of data
acquired. You can also remove existing spectra and control how new spectra
are created.
Tip: The types of chromatogram you use – and the ways in which they are
processed – will depend on your particular situation. Consider your needs and
objectives before deciding which features are going to be most helpful.
Viewing and manipulating chromatograms
6-7
How to display the different types of chromatogram
Displaying different types of chromatogram:
To display this type Do this
of chromatogram
TIC
1. Click Display > Tic.
2. Click the function for which you wish to display
the chromatogram.
3. Click OK.
BPI
1. Click Display > Tic.
2. Click the function for which you wish to display
the chromatogram.
3. Select BPI Chromatogram.
4. Click OK.
Mass
1. Click Display > Mass.
2. Type the mass (m/z) you are interest in into the
Description box.
3. Click the function for which you wish to display
the chromatogram.
4. Click OK.
Analog
1. Click Display > Analog.
2. Click the channel for which you wish to display the
chromatogram.
3. Click OK.
Tips:
6-8
•
In the Options dialog box, you can specify the types of chromatogram
that should appear by default. Open this dialog box by clicking on the
Tools tab of the MassLynx bar, then clicking Options.
•
You can apply advanced chromatogram display settings automatically to
the Chromatogram window by using Chrotool. See Automating
chromatogram display with Chrotool on page 6-11 for further details.
Viewing, processing and storing results
Choosing whether to add traces, replace traces, or create a new
window
Many of the operations you perform in the Chromatogram window – including
displaying different types of chromatogram – will create a new chromatogram
trace.
You can choose whether to add the new trace to the current window (the
default setting), replace the current trace with the new one, or create the new
trace in another window within the Chromatogram window.
Setting new traces display options:
To
Do this
Add the trace
Make sure neither the
nor
tool bar buttons are selected.
Replace the current trace
Select the
tool bar button
Create the trace in a new window
Select the
tool bar button
Removing chromatograms from the display
Removing chromatograms from the display does not alter the saved data – you
are always able to recreate the removed chromatogram.
To remove a single chromatogram from the display:
1.
Activate the chromatogram you want to remove by clicking on it.
Result: The active trace indicator should appear beside it at the left of
the window.
2.
Press the Delete key on the keyboard.
3.
Click OK to confirm that you want to remove the chromatogram.
To remove multiple chromatograms from the display:
1.
Click Display > Remove.
2.
In the Remove Chromatogram dialog box, click the chromatograms you
want to remove.
3.
Click OK.
Viewing and manipulating chromatograms
6-9
Processing your chromatograms
You can manipulate your chromatograms to highlight the areas of most
interest, reduce background noise, and improve presentation.
Three processes are available for use on chromatograms:
•
Background Subtract (polynomial background subtraction)
•
Smoothing
•
Integration
Background subtraction and smoothing help to improve the presentation of
the data. Integration locates peaks, positions baselines and calculates peak
statistics for quantitative work.
A short overview of each of these is given below. For detailed information on
all the settings available, refer to the main online MassLynx Help.
Background subtraction
Background Subtract fits a smooth curve through the noise in the
chromatogram trace then subtracts this curve from the chromatogram,
leaving the peaks on a flat baseline.
To perform a background subtract:
1.
In the Chromatogram window, click Process > Subtract.
2.
Set the options required. The main MassLynx Help provides detailed
information on the meaning of each option.
3.
Click OK.
Smoothing
Smoothing improves presentation and aids interpretation of a chromatogram
by increasing the apparent signal-to-noise ratio.
Two types of smoothing are available for chromatograms: Moving Mean and
Savitzky Golay. Both methods slide a ‘window’ along the chromatogram,
averaging the data points in the window to produce a point in the smoothed
chromatogram.
Moving Mean takes the arithmetical mean of the intensities of the data points
in the window.
6-10
Viewing, processing and storing results
Savitzky Golay takes an average of the intensities weighted by a quadratic
curve. This tends to enhance peak and valley shapes, as well as preserving the
height of the peaks better than the Moving Mean. However, Savitzky Golay
does tend to produce small artifacts on either side of the real peaks.
To perform smoothing:
1.
In the Chromatogram window, click Process > Smooth.
2.
Set the size of the window, the number of smooths, and the smoothing
method.
3.
Click OK.
Integration
The integrate process locates peaks, positions baselines and calculates both
the heights and areas of the peaks above their baselines. There are two
possible integration methods available – the normal algorithm and the Apex
peak integration algorithm.
Both methods can be preceded by smoothing, and a thresholding process can
be applied after integration. The thresholding process can reject peaks, based
on whether their height (or area) is less than an absolute value, or less than a
specified fraction of the height (or area) of the largest peak.
To perform integration:
1.
In the Chromatogram window, click Process > Integrate.
2.
Set the options required. The main MassLynx Help provides detailed
information on the meaning of each option.
3.
Click OK.
Tip: To integrate multiple chromatograms at once – on data already acquired
or as part of the acquisition process – you should use QuanLynx.
Automating chromatogram display with Chrotool
You can save display options and apply them to the Chromatogram window,
either manually or automatically, by using Chrotool. This is particularly
useful if you often want to show a certain type of chromatogram – the
chromatogram for a certain mass, for instance. It may also be useful if the
Viewing and manipulating chromatograms
6-11
chromatogram displayed by default when the Chromatogram window opens is
not the most appropriate for your needs.
Open Chrotool from the Chromatogram window by clicking Display >
ChroTool.
Chrotool allows you to save and apply all of the options that can be set when
creating a TIC, BPI, Mass, or Analog chromatogram. These options can then
be applied to the Chromatogram window either manually – by clicking the
saved settings in Chrotool – or automatically when the Chromatogram
window is opened.
Detailed information on using Chrotool is available in the main online
MassLynx Help.
6-12
Viewing, processing and storing results
Viewing and manipulating spectra
You can view the spectra of the data acquired from running samples. The
Spectrum window shows the mass of ions (or, to be more exact, the
mass-to-charge ratio of those ions) detected during data acquisition.
The data acquired will usually be made up of a number of scans performed in
very rapid succession. Each scan produces a spectrum: you can use the
Spectrum window to step through the data obtained during the scans, or see
the results of a number of scans on screen at one time.
Opening the Spectrum
Spectra acquired and saved in your data files are viewed using the Spectrum
window.
To open the Spectrum window:
1.
In the Sample List, click the number to the left of the sample you wish to
view, so that the whole row is highlighted. You can choose more than one
sample by clicking to the left of the first sample and dragging to the last.
2.
On the Sample List menu bar, click Spectrum.
You will now see the spectrum acquired for the first scan of the selected
sample. The mass-to-charge ratio (m/z) is shown along the x axis (horizontal)
and intensity is shown along the y axis (vertical).
Viewing and manipulating spectra
6-13
There are several important areas on the screen to note:
The Spectrum window:
Data file name
Time of scan
Active spectrum indicator
Function (type of scan)
Number of ions detected at
the largest peak displayed
Tips:
•
The information displayed in the Spectrum window can be configured by
clicking Display > View > Header. For information on how to use this
feature, refer to the MassLynx Help.
•
You can also open the spectrum from the Chromatogram window. For
details, see Using the Chromatogram on page 6-5.
Using the Spectrum
To enable you to focus on the most important areas of the results, the
Spectrum display can be changed in a number of ways. Some of the most
commonly used are:
•
6-14
Showing only part of the spectrum
Viewing, processing and storing results
•
Magnifying the spectrum
•
Opening the chromatogram relating to a single mass, or range of
masses, shown on the spectrum
Showing part of the spectrum
To show part of the spectrum:
1.
Click on the furthest left part of the spectrum you wish to see.
2.
Drag to the furthest right part of the spectrum you wish to see; a line
will be drawn to show how much of the spectrum will be displayed.
3.
Release the mouse button; the spectrum display will be updated.
Alternative: Click Display > Range > From to set the beginning and end mass
values manually.
To revert to seeing all of the spectrum, click the
Display > Range > Default, and click OK.
tool bar button, or click
Magnifying the spectrum
To magnify the spectrum:
1.
Activate the spectrum you want to magnify by clicking on it; the active
spectrum indicator should appear beside it at the left of the window.
2.
Click the
tool bar button; the spectrum will be magnified, with the
degree of magnification indicated at the top left of the spectrum.
3.
To magnify the spectrum further, click the button again.
To reduce the degree of magnification, click the
tool bar button.
To magnify part of the spectrum:
1.
Activate the spectrum you want to magnify by clicking on it; the active
spectrum indicator should appear beside it at the left of the window.
2.
Click Display > Range > Magnify.
3.
In the Spectrum Magnify dialog box, type a custom magnification in the
By box.
4.
In the From and To boxes, type the masses to which you would like to
apply the magnification.
Viewing and manipulating spectra
6-15
5.
To specify a different magnification for another mass range, select
another number from the Range list, then repeat steps 3 and 4.
6.
Click OK.
To revert to seeing the spectrum without magnification, click the
button.
tool bar
Opening a chromatogram from the spectrum
Opening the chromatogram for a single mass
To open the chromatogram for a single mass shown on the spectrum,
right-click on the point of the spectrum you want to see the chromatogram for.
The Chromatogram window will appear, showing the relevant chromatogram.
You can open further chromatograms in the Chromatogram window by
right-clicking on other points on the spectrum.
Opening the chromatogram for a range of masses
You can also display a chromatogram relating to a range of masses displayed
on your spectrum.
To display a chromatogram for a range of masses:
1.
Right-click on the smallest mass you wish to include.
2.
Drag to the largest mass you wish to include; a line will be drawn to
show the extent of the masses that will be included. The mass range will
also be indicated in the status bar at the bottom left of the Spectrum
window.
3.
Release the mouse button; the Chromatogram window will display the
chromatogram for the mass range.
Displaying spectra
You can choose to display the spectrum for a specific time, remove existing
spectra, and control how new spectra are created.
Tips:
•
6-16
The ways in which you display and process the spectra will depend on
your particular situation: consider your needs and objectives before
deciding which features are going to be most helpful.
Viewing, processing and storing results
•
Some of the processing options outlined below will only appear if the
operation can be performed on the type of data you have acquired.
How to display the spectrum for a specific retention time
When you open the Spectrum window from the Sample List, the spectrum for
the first scan of the data acquisition is displayed.
To display the spectrum for a specific retention time:
1.
Click Display > Spectrum > At.
2.
In the Display RAW Spectrum dialog box, type the time for which you
want to display the spectrum, and select the desired function.
3.
Click OK; the spectrum acquired at the time nearest to the time
specified is displayed.
Tip: You can also display the spectrum for a specific retention time by
right-clicking on that time on the chromatogram trace for the data. For details
on how to do this, see Opening a spectrum from the chromatogram trace on
page 6-6.
Choosing whether to add spectra, replace spectra, or create a new
window
Many of the operations you perform in the Spectrum window – including
displaying different spectra for different times – will create a new spectrum on
the screen.
You can choose whether to add the new spectrum to the current window (the
default setting), replace the current spectrum with the new one, or create the
new spectrum in another window within the Spectrum window.
Setting new spectra display options:
To
Do this
Add the spectrum
Make sure neither the
nor
tool bar buttons are selected.
Replace the current spectrum
Select the
tool bar button
Create the spectrum in a new window Select the
tool bar button
Viewing and manipulating spectra
6-17
Removing spectra from the display
Removing spectra from the display does not alter the saved data – you are
always able recreate the removed spectrum.
To remove a single spectrum from the display:
1.
Activate the spectrum you want to remove by clicking on it; the active
spectrum indicator should appear beside it at the left of the window.
2.
Press the Delete key on the keyboard.
3.
Click OK to confirm that you want to remove the spectrum.
To remove multiple spectra from the display:
1.
Click Display > Remove.
2.
In the Remove Spectra dialog box, click the spectra you want to remove.
3.
Click OK.
Processing your spectra
A number of features are available to enhance the clarity of your spectra,
helping you to analyze and share your results more effectively.
Spectrum processing features:
6-18
Process
Description
Refine
Automatically removes
Click Process > Refine
background ions from a
spectrum, thereby allowing it to
be more easily identified – by
library search, for example.
The Refine process operates on
centroid-mode data only.
Viewing, processing and storing results
How to
Spectrum processing features:
Process
Description
How to
Combine
Produces a single spectrum by
subtracting averaged
background spectra from the
average of the spectra from a
TIC peak. The combined scan
exhibits enhanced
signal-to-noise and improved
mass accuracy.
The Combine spectra process
operates on centroid-mode or
continuum data.
Click Process > Combine
Background
subtract
Click Process > Subtract
Adjusts the zero level in a
continuum spectrum to lessen
the effect of chemical noise,
Chemical noise can be caused by
occurrences such as column
bleed.
Background subtract improves
presentation and aids
interpretation.
Smooth
Reduces the high-frequency
Click Process > Smooth
noise present in a spectrum,
thus aiding interpretation.
Data should be smoothed before
mass measurement is
attempted with the Center
process, otherwise peaks may be
created from the noise spikes.
Viewing and manipulating spectra
6-19
Spectrum processing features:
Process
Description
How to
Center
Uses all the points across a peak Click Process > Center
in a continuum trace to
calculate the mass of the peak
center.
The centering process can be
used either to label each peak
with the calculated mass, or to
produce a single bar from each
peak in a continuum spectrum.
Mass measure
Performs a combination of
Click Process > Mass
background subtraction,
Measure
smoothing, and centering in one
command.
Integrate
Locates spectral peaks, draws
baselines and calculates peak
areas. Spectrum integration
works over the full mass range
of the spectrum.
Click Process >
Integrate
Transform
Uses charge states assigned to
each peak to display the m/z
spectrum on a true molecular
mass axis.
Rule: Transform will only be
available if it was selected
during installation.
Click Process >
Transform
MaxEnt
Uses the maximum entropy
method to produce true
molecular mass spectra from
multiply-charged ElectroSpray
spectra.
Rule: MaxEnt will only be
available if it was selected
during installation.
Click Process >
MaxEntn
Detailed information on the settings that apply to each of these processing
features is supplied in the main MassLynx Help.
6-20
Viewing, processing and storing results
Processing and interpreting data
The data acquired from your instruments can be processed and distributed in
many different ways to provide the information you need. As there are many
different uses for mass spectrometry, MassLynx provides a range of utilities
that assist with these various needs: these utilities are known as Application
Managers.
The Application Managers available will depend on your organization’s
priorities. Data processing with two Application Managers – QuanLynx and
OpenLynx – is available to all users, and will be accessible so long as these
Application Managers were selected at installation time.
Tip: If QuanLynx and OpenLynx were not installed during the initial
MassLynx installation, they can be added to the system at any time. For
details, see Installing additional Application Managers on page 1-6.
Quantitation using QuanLynx
QuanLynx is used to quantify samples – to determine how much of a known
compound is in a sample.
To do this, QuanLynx compares the data acquired with a calibration curve –
representing the known values for different amounts of the compound – and
then calculates the quantity of the compound found in the sample.
To access QuanLynx, click the QuanLynx tab on the left of the MassLynx
Shortcut bar.
For a quick start guide to QuanLynx, see the online QuanLynx Help.
Providing access and distributing results using OpenLynx
OpenLynx is a versatile Application Manager providing report generation and
distribution features, alongside capabilities for walk-up access and
submission of samples using the optional OALogin module.
To access OpenLynx, click the OpenLynx tab on the left of the MassLynx
Shortcut bar.
For a quick start guide to OpenLynx, see the online OpenLynx Help.
Processing and interpreting data
6-21
Processing data using other Application Managers
One or more other Application Managers may be installed on your system.
Each Application Manager will appear as another tab on the left of the
MassLynx shortcut bar. To access an Application Manager, click the tab; the
MassLynx bar will show icons linking you to the features available.
Assistance is available for each Application Manager by clicking the question
mark
to the right of the Application Manager’s name in the MassLynx
bar.
6-22
Viewing, processing and storing results
Storing results in SDMS
The results you obtain will be stored in the project that was used to acquire
them. They can be opened from within the project, and you can also view data
from other projects in the Chromatogram and Spectrum windows by browsing
to the data files of interest.
If you have Waters NuGenesis SDMS (Scientific Data Management System)
the data acquired through MassLynx can be shared by sending it to SDMS.
Data can also be retrieved from SDMS for viewing and processing in
MassLynx.
Configuring MassLynx SDMS settings
MassLynx SDMS settings need to be configured before you can start sending
and retrieving data.
To configure SDMS settings:
1.
Click the SDMS tab on the left of the MassLynx Shortcut bar.
2.
Click Configure.
3.
Enter the location of the archive folder.
Tip: Your SDMS system will need to be configured to monitor the
directory specified here.
4.
Select the file types that you want to be available for sending to SDMS.
Tip: While selecting View All Files will allow all file types to be seen in
the Send dialog box, it will only be possible to send the specific file types
selected.
5.
Type the URL of the NuGenesis Vision Browser, used to retrieve
information.
Tip: Check that you have entered the URL correctly by clicking the
Launch button.
6.
Click OK.
Storing results in SDMS
6-23
Sending data to SDMS
When you are ready to send data to SDMS, it is possible to choose which files
should be sent and whether the originals should be removed.
To send data to SDMS:
1.
Click the SDMS tab on the left of the MassLynx Shortcut bar.
2.
Click Send.
3.
Browse to the location of the data you wish to send.
4.
In the drop-down list on the right of the dialog box, click the type of file
you want to send.
Tip: Only the types of file specified in the Configure dialog box will be
available.
5.
In the list of available files at the top right of the dialog box, click the
files you wish to send, then click Add to Archive. Alternatively, click Add
All to add all of the files in the available files list.
Result: The files you have specified are shown in the Archive File List at
the bottom of the dialog box. These are the files that will be made
available to SDMS when you click Send.
6.
Repeat steps 3 to 5 for additional files you wish to send.
7.
If you want to remove the original files from disk, select Remove
Original.
8.
Click Send.
Requirement: For the data to be successfully archived, SDMS will need to be
correctly set up to monitor the configured archive folder.
Retrieving data from SDMS
You retrieve data using the NuGenesis Vision Browser. If it has been
configured, you can access the Browser by clicking the SDMS tab on the left of
the MassLynx Shortcut bar, then clicking Retrieve.
Help on locating, viewing, and restoring your data can is available by clicking
the question mark button in the Vision Browser.
6-24
Viewing, processing and storing results
A
Additional OpenLynx installation
instructions
This appendix provides installation instructions for OpenLynx Login,
OpenLynx Toolkit, and the Diversity browser.
Key disks are required to install these components. You will be asked to
enter the location of the key disk during the installation process. If you
do not have an appropriate key disk – and believe you should – contact
your MassLynx system administrator.
Contents:
Topic
Page
Installing OpenLynx Login
A-2
Installing OpenLynx Toolkit
A-5
Installing Diversity browser
A-22
A-1
Installing OpenLynx Login
Requirements:
•
Before installing OpenLynx Login, you must install MassLynx on the PC
controlling the mass spectrometer. Refer to Installing MassLynx on
page 1-4 for details.
•
The OpenLynx Login PC must be able to communicate with the
MassLynx PC. If OpenLynx Login is installed on a different PC to
MassLynx, a network connection is required.
There are three steps to installing OpenLynx Login:
1.
Sharing the installation directory on the MassLynx PC.
2.
Mapping a drive on the OpenLynx Login PC to the MassLynx PC.
3.
Installing OpenLynx Login on the OpenLynx Login PC.
Sharing the installation directory on the MassLynx PC
To share the installation directory on the MassLynx PC:
1.
Open Windows® Explorer, right-click the directory that MassLynx was
installed into (usually C:\MassLynx), then click Properties.
2.
Click the Sharing tab.
Tip: If a warning message is displayed, click If you understand the risk
but still want to share the root of the drive, click here to open the
Sharing page.
3.
Select Share this folder.
4.
Enter a name in the Share name box.
5.
Click Apply.
Tip: If a warning message is displayed because the share name is too
long, select the appropriate response and amend the share name.
6.
Click OK.
Result: The directory is shared. In Windows Explorer, the directory now
shows a hand under the folder icon.
A-2
Mapping a drive on the OpenLynx Login PC to the MassLynx PC
To map the drive:
1.
On the PC on which you wish to install OpenLynx Login, open Windows
Explorer, then click Tools > Map Network Drive.
2.
In the Drive box, click a drive letter without a folder currently mapped
to it (an available drive).
3.
Click Browse, then browse to the MassLynx PC and select the shared
directory created during Sharing the installation directory on the
MassLynx PC on page A-2.
4.
Click Finish.
Result: The shared directory is mapped to the drive letter selected.
Installing OpenLynx Login
To install the OpenLynx Login program on the login PC:
1.
Log on to the PC using a user account with permission to install
software – usually an administrator account.
2.
Insert MassLynx 4.1 CD 2 into the appropriate drive.
3.
Use Windows Explorer to navigate to the OALogin directory, then
double-click setup.exe; the OALogin installer is displayed.
4.
Click Next, confirm that you accept the license agreement, then click
Next again to accept the installation directory for OALogin.
5.
On the MassLynx Folder page, click Change, then Browse to the
MassLynx installation directory. If you are installing on a PC other than
the MassLynx PC, this will be the drive that was mapped during
Mapping a drive on the OpenLynx Login PC to the MassLynx PC on
page A-3.
6.
Click Next, then click Install to begin the installation process.
Tip: If an OALogin - Wizard error message is displayed, stating that the
selected directory does not contain a valid MassLynx installation, click
OK, then repeat step 7.
Installing OpenLynx Login
A-3
7.
When prompted, browse to the location of the key disk that has been
supplied. If you do not have the appropriate key disk, contact your
MassLynx system administrator.
Result: OpenLynx Login is installed.
A-4
Installing OpenLynx Toolkit
OAToolkit enables administrators to manage OALogin users from a
single PC, and monitor the status of Acquisition PCs.
The OAToolkit software comprises:
•
Administration Tool — Enables an administrator to create and
manage all OALogin users from a single PC, and to replicate that
information to multiple OALogin PCs and Acquisition PCs.
•
OAToolkit Service — Runs in the background on one or more
Acquisition PCs, monitors sample batches submitted by OALogin
users that were uploaded from the Administration Tool, and
automatically:
–
relocates data produced during the processing of an OALogin
user's batch of samples.
–
creates new project folders in which to store the processing data
on a timed basis.
–
converts report files to different formats (XML and HTML, for
example,).
Tip: Settings that you can customize in the Administration Tool
enable the service to perform these automatic actions.
•
Remote Status Monitor — Enables any user to monitor the status of
multiple instruments and their batch queues from a single PC.
This section describes a typical hardware setup and how to install and
set up the software.
Contents:
Topic
Page
Typical hardware setup for OAToolkit
A-6
Installing the software
A-6
Setting up the OAToolkit Service
A-7
Remote Status Monitor
A-13
Installing OpenLynx Toolkit
A-5
Typical hardware setup for OAToolkit
This section describes the typical hardware setup. Logically, there are four
PCs:
•
Acquisition PC — a PC that has MassLynx and the OAToolkit Service
running, and is attached to an instrument.
•
OALogin PC — any regular OALogin Terminal which is normally used
to log samples on the Acquisition PC.
•
File Storage PC — a PC on the same network domain as the Acquisition
PC that will be used to store files moved from the Acquisition PC by the
OAToolkit Service.
•
Administration PC — a PC that has the OAToolkit Administration Tool
installed.
It is not necessary to have four separate PCs to run the OAToolkit. You can,
for example, use the same PC to run the OAToolkit Administration Tool and
to store the files sent from the OAToolkit service. However, for the scope of
this discussion, each PC is treated as a separate entity.
Installing the software
To run OAToolkit, you need to install the Administration Tool on the
Administration PC, and the OAToolkit Service on the Acquisition PC.
Installing the OAToolkit Administration Tool on the Administration PC
To install the OAToolkit Administration Tool:
1.
At the Administration PC, insert MassLynx 4.1 CD 2.
2.
Browse to the OAToolkit directory, then double-click setup.exe.
3.
In the dialog, select the check box OAToolkit Administration Tool.
4.
In the dialog, select the default installation directory of C:\OAToolkit.
5.
When prompted, browse to the location of the key disk that has been
supplied. If you do not have the appropriate key disk, contact your
MassLynx system administrator.
When the installation has finished, there is a directory C:\OAToolkit on the
Administration PC.
A-6
Installing the OAToolkit Service on the Acquisition PC
To install the OAToolkit Service:
1.
At the Administration PC, insert MassLynx 4.1 CD 2.
2.
Browse to the OAToolkit directory, then double-click setup.exe.
3.
In the dialog, select the check box OAToolkit Service.
4.
In the dialog, select the default installation directory of C:\OAToolkit.
5.
When prompted, browse to the location of the key disk that has been
supplied. If you do not have the appropriate key disk, contact your
MassLynx system administrator.
When the installation has finished, there is a directory C:\OAToolkit on the
Acquisition PC, and the OAToolkit Service is running.
Setting up the OAToolkit Service
The OAToolkit Service monitors batch files that have been processed on the
Acquisition PC. When the service locates a batch file that belongs to a
recognized OALogin user, it transfers the raw data files, report files, batch
files, and so on, that are associated with that sample. Typically, most
OAToolkit administrators would want these files moved to a separate File
Storage PC, not the Acquisition PC.
This section details how to set up one Acquisition PC and one File Storage PC
to which the OAToolkit will transfer files.
Requirement: Both PCs must be on the same network domain.
Setting Up the OAToolkit Service on the Acquisition PC
To enable the service to transfer data to File Storage PCs on the same
network, the OAToolkit service must be logged in as a domain user.
To log in the service:
1.
Log in to the Acquisition PC as a local Windows administrator.
2.
On the Windows desktop, select Start > Run. The Run dialog opens.
3.
In the Run dialog, type Services.msc, and then click OK. The Services
dialog opens.
Installing OpenLynx Toolkit
A-7
Setting up the Acquisition PC - OALogin Post Data Processing
Properties (Local Computer) dialog:
4.
In the Services (Local) list, locate the service OALogin Post Data
Processing, and then stop the service.
5.
In the service list, right-click the OALogin Post Data Processing service
and select Properties.
6.
Select the Log On tab.
7.
Select the option This account:, and then type the fully-qualified user
account name and password.
In the example graphic above, the service is being started using the
domain user DOMAIN1\USER1.
A-8
8.
Click Apply, and then click OK.
9.
Start the service.
In the example, the service now has all the permissions and the
privileges of the domain user USER1.
10. Log out as the local administrator, and log back in as the normal
Acquisition PC user.
You now need to set up a folder on the File Storage PC so that it is ready to
accept files from the service.
Setting Up the File Storage PC
To set up the File Storage PC:
1.
Log in to the File Storage PC. Ensure that you are logged in as a user
who has rights to create and share directories locally.
2.
Create a directory, for example C:\UserData.
3.
Set up the share permissions on this directory to enable the service user
on the Acquisition PC to have full privileges.
Installing OpenLynx Toolkit
A-9
Setting up the File Storage PC - Permissions dialog - Sharing page:
4.
A-10
Click the Security tab, add the user, and then set full NTFS permissions
for the user.
Setting up the File Storage PC - Permissions dialog - Security page:
5.
On the Security page, click Advanced.
The OAToolkit Service user must have the ability to create directories
underneath the shared directory. For example, the OAToolkit
administrator might need the system to create directories for specific
users such as UserData\User1 and UserData\User2. To enable this,
you use the advanced security settings.
Installing OpenLynx Toolkit
A-11
Setting up the File Storage PC - Permissions dialog - Advanced
Security - Permissions page:
6.
On the Advanced Security Settings - Permissions page, select the user in
the list.
7.
Clear the check box Inherit from parent the..., and select the check box
Replace permission entries on all child objects...
This gives the OAToolkit Service user full control over sub-folders.
8.
A-12
Click OK in all dialogs to exit.
Remote Status Monitor
The Remote Status Monitor (RSM):
•
Monitors the state of one or more Acquisition PCs.
•
Writes monitoring information to an XML file, which is then read by an
HTML page. The information can then be viewed in a Web browser.
This section refers to two different computers:
•
Administration PC — a PC that has the Remote Status Monitor
software installed.
Requirement: This PC must be powered up at all times and be available
to monitor instruments.
•
Acquisition PC — any MassLynx PC which is being monitored.
Installing Remote Status Monitor
To install Remote System Monitor:
1.
At the Administration PC, insert MassLynx 4.1 CD 2.
2.
Browse to the OAToolkit directory, then double-click setup.exe.
3.
In the OAToolkit wizard:
4.
•
Accept the terms of the license agreement.
•
Select to install the OAToolkit Remote Status Monitor.
•
Install the application in the folder C:\OAToolkit.
When prompted, browse to the location of the key disk that has been
supplied. If you do not have the appropriate key disk, contact your
MassLynx system administrator.
When the installation has completed, there is a directory
C:\OAToolkit\Remote Status Monitor\WebService on the Administration
PC. Within this directory, there is a file named default.htm; this is the file
that is used to monitor the instruments through a Web browser.
Installing OpenLynx Toolkit
A-13
Location of default.htm in OAToolkit:
Setting up, registering and monitoring instruments
Requirement: Your company network administrator should be present when
these procedures are being performed.
To have a configuration that proves that the RSM is running correctly, there
should be at least one Administration PC, and one Acquisition PC.
Any Acquisition PC that is to be monitored must be set up so that MassLynx
writes to its status file. This is not a default option on installation of
MassLynx.
To set up the Acquisition PC for monitoring:
A-14
1.
On the Acquisition PC, start MassLynx.
2.
From the MassLynx Shortcut Bar Menu, click Tools, and then from the
Shortcut Bar, click Options.
3.
In the Options dialog, click the System tab.
4.
On the System page MassLynx Status options, ensure that the following
are set:
•
Update Status is selected.
•
Refresh Rate = 5 seconds
•
File Name is C:\MassLynx\status.ini
MassLynx Status options:
5.
Click OK, and then restart MassLynx.
This Acquisition PC is now ready to be monitored.
Registering and monitoring instruments
To monitor the instrument, you must register the instrument with Remote
Status Monitor (RSM). This enables you to run RSM and view the results.
Requirement: The user on the Administration PC must have read privileges
to the directory C:\MassLynx on the Acquisition PC. This enables RSM on the
Administration PC to read the Status.ini file.
Installing OpenLynx Toolkit
A-15
To register and monitor instruments:
1.
On the Administration PC, select:
Start > All Programs > OAToolkit Remote Status Monitor
The main Remote Status Monitor screen opens.
2.
To register the instrument, click
Configuration dialog opens.
. The Add/Modify Instrument
Remote Status Monitor - Add/Modify Instrument Configuration dialog:
3.
In the Device Name text box, type a unique ID.
This name will be displayed in all pages of the RSM to identify the
instrument.
4.
In the MassLynx Location text box, type the path, or browse to the
location of MassLynx on the Acquisition PC.
5.
Click OK.
The instrument details are displayed in the list on the main RSM
screen.
6.
A-16
To start monitoring, click
. If the instrument is on-line, functioning
but not acquiring, the status is Idle.
Remote Status Monitor - instrument registered and monitored:
Viewing instrument details in a Web browser
To view the default.htm file, which shows instrument details in a Web
browser, you must create a virtual directory on the Windows Internet
Information Services (IIS) on the Administration PC.
Tip: If IIS is not installed on the Administration PC, please refer to the
Windows documentation.
The RSM writes status and batch information for the instrument(s) to its
internal XML files, which are read by the default.htm file.
To create a virtual directory on IIS:
1.
In the Windows operating system, select Start > Control Panel >
Administrative Tools.
Installing OpenLynx Toolkit
A-17
Windows Administrative Tools list:
2.
Click Internet Information Services.
The Internet Information Services window opens.
Windows Internet Information Services window:
A-18
3.
Expand the local computer tree, and then click Web Sites.
Windows Internet Information Services - Web sites list:
4.
In the table, right-click Default Web Site, and then select New > Virtual
Directory...
The Virtual Directory Creation wizard opens.
5.
In the wizard:
•
Type a name for the virtual directory, such as InstrumentInfo.
•
Browse to the directory that contains the default.htm file
C:\OAToolkit\RemoteStatusMonitor\WebService
•
Select the check boxes for the access permissions Read, Run scripts
(such as ASP), and Browse.
To view instrument details in Web browser
1.
In a Web browser, type the URL
http:\\<Administration PC name>\<virtual directory
alias>\default.htm
The Status Summary page opens in the browser and contains a list of
Acquisition PCs and the number of samples in their queues in a table.
The colors are:
Red = the instrument is inactive
Green = the instrument is active
Amber = the instrument is off line.
Installing OpenLynx Toolkit
A-19
Remote Status Monitor - Status Summary page:
2.
A-20
To display more detailed information about an instrument, click
anywhere in the instrument row. An instrument summary page opens.
Remote Status Monitor - instrument details:
3.
To return to the Status Summary, click Summary Page at the top-right
corner of the page.
Installing OpenLynx Toolkit
A-21
Installing Diversity browser
Diversity browser is used to view, create, or print reports on a PC that does
not have MassLynx installed on it.
To install Diversity browser:
1.
Log on to the PC using a user account with permission to install
software – usually an administrator account.
2.
Insert MassLynx 4.1 CD 2 into the appropriate drive.
3.
Use Windows Explorer to navigate to the Diverse directory, then
double-click setup.exe; the Diversity Browser installer is displayed.
4.
Click Next, confirm that you accept the license agreement, then click
Next again to accept the installation directory for Diversity Browser.
5.
Click Install to begin the installation process.
6.
When prompted, browse to the location of the key disk that has been
supplied. If you do not have the appropriate key disk, contact your
MassLynx system administrator.
Result: The Diversity browser is installed.
A-22
Index
A
Acquiring data
Analog 5-2, 5-3
from the Sample List 5-3
from the Tune window 5-2
MRM data 5-2, 5-3
SIR data 5-2, 5-3
starting a run 5-9
viewing progress 5-10
Acquisition functions 5-3
Acquisition Setup dialog box 5-2
Add chromatogram trace 6-9
Add spectrum 6-17
Adding rows to the Sample List 5-6
Administration Tool
OAToolkit A-5
Analog chromatograms 6-3, 6-8, 6-11
Analog data 5-2, 5-3
Application Managers 6-2, 6-21
installing 1-6
Sample Lists 5-4, 5-5
Archiving results 6-23
Automating display of chromatograms
6-11
Autosampler 1-7, 4-6
Autosampler Bed Layout 5-6
AutoTune wizard 4-3, 4-5, 5-3
B
Background subtraction 6-10, 6-19
Basic Security 1-4, 1-5
BPI chromatograms 6-3, 6-8, 6-11
C
Calibration 4-5
TOFs 4-5
Calibration wizard 4-5
Center spectra 6-20
Chromatogram window 6-4
Chromatograms
automating display of 6-11
background subtraction 6-10
integration 6-11
magnifying 6-5
new trace options 6-9
opening from spectra 6-16
opening spectra from 6-6
processing 6-10
removing 6-9
showing part of 6-5
smoothing 6-10
types of 6-3, 6-8
viewing 6-3
viewing during acquisition 5-10
Chrotool 6-8, 6-11
Columns
customizing the Sample List
display 5-4, 5-8
minimum Sample List
requirements 5-5
Combine spectra 6-19
Contacting Waters 1-iii
Copyright 1-ii
Creating
projects 3-2
Sample Lists 5-4
Customizing the Sample List 5-8
D
Data
acquisition 5-1
files 3-4
processing 6-21
storing in SDMS 6-23
Index-1
viewing 6-3, 6-13
Data acquisition
from the Sample List 5-3
from the Tune window 5-2
starting 5-9
viewing progress of 5-10
Deleting
chromatograms 6-9
spectra 6-18
Detector 1-7, 4-6
Directories
in a project 3-4
Display options
saving 6-11
Displaying chromatograms
automatically 6-11
Diversity browser 1-4
installing A-22
I
Importing data to the Sample List 5-8
Information bar 2-3
Inlet methods 4-6, 4-7, 5-2, 5-3, 5-4
specifying in the Sample List 5-7
Installer 1-2
Installing
Application Managers 1-6
Diversity browser A-22
MassLynx 1-2, 1-4
OpenLynx Login A-2
OpenLynx Toolkit A-5
Instrument configuration 4-6
Integrating chromatograms 6-11
K
Key disks 1-4
L
Events and Triggering 4-7
Experiment Setup window 5-3
LC 1-7, 4-6
Liquid chromatograph 1-7, 4-6
Login dialog box 2-2
F
M
E
Fill down 5-6
Fill series 5-6
Folders
in a project 3-4
Full Security 1-4, 1-5, 1-6
Functions 5-3
G
Gas chromatograph 1-7, 4-6
GC 1-7, 4-6
H
Hidden columns
in the Sample List 5-4
HPLC 1-7, 4-6
Index-2
Magnifying chromatograms 6-5
Magnifying spectra 6-14
Mass calibration 4-5
Mass chromatograms 6-3, 6-8, 6-11
Mass measure 6-20
Mass spectrometer 1-7
tuning 4-2
MassLynx
installation 1-4
security 1-4, 1-5, 1-6
starting 2-2
window 2-3
MaxEnt 6-20
Menu bar 2-3
Moving Mean 6-10
MRM 5-2, 5-3
MS methods 5-3, 5-4
specifying in the Sample List 5-7
MS Tune 4-2, 4-5, 5-2
Multiple Reaction Monitoring 5-2, 5-3
N
Network
sharing A-2
New project 3-2
New window for chromatogram 6-9
New window for spectrum 6-17
NuGenesis SDMS 6-2, 6-23
O
OALogin 1-4
installing A-2
OAToolkit 1-4
Administration Tool A-5
installing A-5
Remote Status Monitor A-5
Service A-5
Opening chromatograms from spectra
6-16
Opening MassLynx 2-2
Opening spectra from chromatograms
6-6
OpenLynx 6-2, 6-21
batch files 5-8
installation 1-4
OpenLynx Login
installing A-2
OpenLynx Toolkit
see OAToolkit
Operate 5-2, 5-9
P
PDA detector 1-7, 4-6
Processing
chromatograms 6-10
data 6-21
spectra 6-18
Project
creating 3-2
structure 3-4
Pump 1-7, 4-6
I
Q
QuanLynx 6-2, 6-21
installation 1-4
integrating chromatograms 6-11
Sample Lists 5-4
Queue
button 2-4
viewing data acquisition 5-10
R
Real time update 5-10
Reference file 4-5
Remote Status Monitor
OAToolkit A-5
Removing chromatograms 6-9
Removing spectra 6-18
Replace chromatogram trace 6-9
Replace spectrum 6-17
Resolution 4-2
Results
storing in SDMS 6-23
viewing 6-3, 6-13
Rows
adding to the Sample List 5-6
S
Sample List 2-3, 5-2
acquiring data 5-3, 5-9
adding rows 5-6
Autosampler bed layout 5-6
copying data into 5-7
creating 5-4
customize display 5-4
customizing the display 5-8
Index-3
Fill down 5-6
Fill series 5-6
hidden columns 5-4
importing 5-8
minimum requirements 5-5
specifying inlet methods 5-7
specifying MS methods 5-7
viewing chromatograms from 6-4
viewing spectra from 6-13
Savitzky Golay 6-10
Scans 5-3, 6-13
SDMS 6-2, 6-23
installation 1-4
Security 1-4, 1-5, 1-6
Selected Ion Recording 5-2, 5-3
Sensitivity 4-2
Sharing network drive A-2
Shortcut button 2-4
SIR 5-2, 5-3
Smooth spectra 6-19
Smoothing chromatograms 6-10
Solvent Delivery System 1-7, 4-6
Spectra
Background subtract 6-19
Center 6-20
Combine 6-19
magnifying 6-14
Mass measure 6-20
MaxEnt 6-20
new spectrum options 6-17
opening chromatograms from 6-16
opening from chromatograms 6-6
processing 6-18
removing 6-18
showing part of 6-14
Smooth 6-19
Transform 6-20
viewing 6-13
Spectrum
Index-4
viewing during acquisition 5-10
Spectrum window 6-13
Start Sample List Run dialog 5-9
Starting MassLynx 2-2
Status button 2-4
Storing results in SDMS 6-23
Structure of projects 3-4
Subtract 6-10, 6-19
T
TIC chromatograms 6-3, 6-8, 6-11
Tool bar 2-3
Total Run Time 5-3
Trademarks 1-ii
Transform spectra 6-20
Tune window 4-2, 4-5, 5-9
acquiring data 5-2
Tuning 4-2, 5-4
U
UPLC 1-7
UV detector 1-7, 4-6, 6-3
V
Viewing
chromatograms 6-3
data acquisition 5-10
spectra 6-13
W
Waters
contacting 1-iii
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