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Masslynx User Guide

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Masslynx User Guide

Separation Science offers free learning from the experts covering methods, applications, webinars, eSeminars, videos, tutorials for users of liquid chromatography, gas chromatography, mass spectrometry, sample preparation and related analytical techniques. Subscribe to our eNewsletter with daily, weekly or monthly updates: Food, Environmental, (Bio)Pharmaceutical, Bioclinical, Liquid Chromatography, Gas Chromatography and Mass Spectrometry. Follow us on Twitter: @Sep_Science, @Food_Science_, @Pharma_Science_Follow us on Linkedin: -science-/

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 op


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