MassLynx 4.1 Getting Started Guide

1 MassLynx Started Guide71500113203/Revision ACopyright Waters Corporation 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 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.

2 In no event shall Waters Corporation be liable for incidental or consequential damages in connection with, or arising from, its Corporation34 Maple StreetMilford, MA 01757 USAT rademarksMicromass and Waters are registered trademarks, MassLynx is a trademark of Waters trademarks or registered trademarks are the sole property of their respective commentsPlease 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 can reach us at WatersYou will be able to resolve most MassLynx issues yourself.

3 However, if this is not the case, you must contact in the USA and Canada should report maintenance problems they cannot resolve to Waters Technical Service (800 252 4572). All others should visit and click Offices, or phone their local Waters subsidiary or Water corporate headquarters at 34 Maple Street, Milford, MA 01757, 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 receivedTable of ContentsvCopyright notice.

4 Ii Trademarks .. ii Customer comments .. ii Contacting Waters .. iii1 Before you start .. 1-1 Introduction .. 1-2 Installing MassLynx .. 1-4 Installing additional Application 1-6 Preparing the system for use .. 1-72 Starting MassLynx .. 2-1 Opening MassLynx .. 2-2 The MassLynx window .. 2-33 Creating a project .. 3-1 Creating a new project .. 3-2 Understanding project structure .. 3-44 Instrument setup .. 4-1 Tuning your mass spectrometer .. 4-2 What is tuning? .. 4-2 Tuning your instrument.

5 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 ContentsviTable of Contents Specifying your inlet 4-75 Acquiring data .. 5-1 Acquiring data from the tune window .. 5-2 Acquiring data from the sample list .. 5-3 Setting up an MS 5-3 Creating a Sample 5-4 Starting data 5-96 Viewing, processing and storing results.

6 6-1 How to view, process, and store results .. 6-2 Viewing and manipulating chromatograms .. 6-3 Opening the Chromatogram 6-4 Using the Chromatogram .. 6-5 Displaying chromatograms .. 6-7 Processing your chromatograms .. 6-10 Automating chromatogram display with Chrotool .. 6-11 Viewing and manipulating spectra .. 6-13 Opening the 6-13 Using the Spectrum .. 6-14 Displaying spectra .. 6-16 Processing your spectra .. 6-18 Processing and interpreting data .. 6-21 Quantitation using QuanLynx .. 6-21 Providing access and distributing results using OpenLynx.

7 6-21 Processing data using other Application 6-22 Storing results in SDMS .. 6-23 Configuring MassLynx SDMS settings .. 6-23 Sending data to SDMS .. 6-24 Retrieving data from SDMS .. 6-24 Table of ContentsviiA Additional OpenLynx installation instructions .. A-1 Installing OpenLynx Login .. A-2 Sharing the installation directory on the MassLynx PC .. A-2 Mapping a drive on the OpenLynx Login PC to the MassLynx PC .. A-3 Installing OpenLynx Login .. A-3 Installing OpenLynx Toolkit .. A-5 Typical hardware setup for OAToolkit.

8 A-6 Installing the software .. A-6 Setting up the OAToolkit Service .. A-7 Remote Status A-13 Installing Diversity browser .. A-22 Index .. Index-1viiiTable of Contents1-11 Before you startThis chapter will introduce MassLynx , explain installation, and describe what you need to have ready before starting to use the :TopicPageIntroduction1-2 Installing MassLynx1-4 Preparing the system for use1-71-2 Before you startIntroductionMassLynxTM is a powerful software application that configures and controls your Waters mass spectrometer, and provides many features to analyze and process the data 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 following diagram shows the tasks that need to be performed to get up and running with MassLynx .

9 They will be outlined in more detail, step by step, later in the to get Started with MassLynx :Setup yourinstrumentspage 4-1 Create a newprojectpage 3-1 Prepare the system for usepage 1-1 StartMassLynxpage 2-1 Acquire datapage 5-1 View your datapage 6-2 Process yourdatapage 6-21 From the Tune windowpage 5-2 Using the Sample Listpage 5-3 Tuningpage 4-2 Calibrationpage 4-5 Inletspage 4-6MS Methodspage 5-31-4 Before you startInstalling MassLynxIn most cases MassLynx will be installed for you by a Waters engineer. If you already have MassLynx installed, skip this : Before installing MassLynx , refer to the Release Notes for detailed information relating to the release.

10 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 : If you have previously installed Waters Instruments Component Software, uninstall it using Windows Add or Remove Programs.