Masslynx User Guide: A Step-by-Step Tutorial for MassLynx Software Users

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Masslynx User Guide

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One of the most frequent questions from Waters users is if they can use MSe data for molecular networking. Bascially, MSe data is not available for classical molecular networking workflow, because it is a type of data-independent acquisition method so does not include precursor ion information.However, MSe data can be deconvoluted (currently MS-DIAL is the proper software for it) and applied to the FBMN workflow. You can find relevant information here.

10 Introduction MassLynx TM 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

12 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. If MassLynx has been supplied on a CD, or other removable media, insert it into the appropriate drive. 1-4 Before you start

13 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

22 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

31 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

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