MassLynx 4.1 Release Notes

MassLynx 4.1 Release Notes 716001833 / A Copyright Waters Corporation 2005. All rights reserved.

ii 716001833 / A MassLynx 4.1 Release Notes

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, the use of this document. Waters Corporation 34 Maple Street Milford, MA 01757 USA Millennium and Waters are registered trademarks of Waters Corporation. Empower and Breeze are trademarks of Waters Corporation. Agilent is a registered trademark of Agilent Technologies, Incorporated Compaq is a registered trademark of Compaq Computer Corporation. Gilson is a registered trademark of Gilson Corporation. IBM is a registered trademark of IBM Corporation. Identify is a registered trademark of Identify Software, Ltd. IntelliStation is a registered trademark of IBM. JASCO is a registered trademark of JASCO Advanced Chemistry Development Incorporated. National instruments is a trademark of National Instruments Corporation NT is a registered trademark of Microsoft Corporation. Nebula is a trademark of Gilson, Incorporated. Pentium is a registered trademark of Intel Corporation. Roxio is a registered trademark of Sonic Solutions, Incorporated. Shimadzu is a registered trademark of Shimadzu Corporation. MassLynx 4.1 Release Notes 716001833 / A iii

ThinkCentre is a registered trademark of IBM Corporation. UltiMate is a trademark of Dionex Corporation. Windows is a registered trademark of Microsoft Corporation. Windows XP is a registered trademark of Microsoft Corporation. Xeon is a registered trademark of Intel Corporation. Other trademarks or registered trademarks are the sole property of their respective owners. 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. iv 716001833 / A MassLynx 4.1 Release Notes

Read this first MassLynx 4.1 is a full MassLynx version that includes new features and corrects selected faults found in previous releases. It supercedes MassLynx 4.0 and all service packs and software change notes associated with that version. To operate MassLynx software, you must install it on a workstation. See Installing MassLynx 4.1. The scope of MassLynx 4.1 is defined in General Information, on page 5. Additional MassLynx training is available through local Waters subsidiaries. Contact your Waters representative for schedules and other details. Configuring the acquisition PC requires setting up two network interfaces. One communicates with your Waters/Micromass mass spectrometer, which Waterssupplied IBM workstations are configured for and ready to connect to. Confirm the correct network interface is connected to the mass spectrometer, noting the label that identifies the mass spectrometer's RJ45 connector. The other network interface allows connecting to a local network and requires configuring to meet local network requirements. The user documentation set for MassLynx 4.1 is a collection of documents in several formats: Printed hardcopy documentation: The MassLynx 4.1 Getting Started Guide and the MassLynx 4.1 Security Guide accompany the product as printed documents.. Documentation Bookshelf CD: The Documentation Bookshelf CD contains information for managing and using your mass spectrometry software and instruments PDF file: From the Documentation Bookshelf CD, you can access PDF files of user manuals for supported mass spectrometry instruments. The CD also includes PDF files containing additional MassLynx information. Online Help: MassLynx incorporates an HTML-based online Help system, which includes both task-based and overview information. You access Help directly from the software's Help menu or the Documentation Bookshelf CD. From the CD, you can access individual MassLynx Application Manager Help files individually. To enhance quick mastery of the software, several Application Manager Help files include tutorials or quick-start guided tours. MassLynx 4.1 Release Notes 716001833 / A v

vi 716001833 / A MassLynx 4.1 Release Notes

Table of Contents 1 General Information...1-1 Micromass mass spectrometers not supported 1-2 Micromass mass spectrometers supported Full Security installations 1-2 MassLynx application managers supported in Full Security installations 1-2 Operating HPLC Instruments controlled by the National Instruments GPIB controller board (part number 186000825) 1-3 Waters inlets instrument support information 1-3 Unsupported Waters inlets 1-6 Non-Waters inlets instrument support information 1-7 Minimum computer hardware configurations 1-11 Supported operating systems 1-14 PC Power Settings, Hyperthreading, Third-Party Application Compatibility, and Periphera ls 1-15 Serial interface control card 1-16 Antivirus software- 1-16 2 Installing MassLynx 4.1...2-1 General installation procedure 2-1 Installing MassLynx 4.1 with Waters inlets controlled by Ethernet 2-1 Installing MassLynx 4.1 and OALogin 2-2 3 New Features and in MassLynx 4.1...3-1 Mass Spectrometer Enhancements and... 3-1 All mass spectrometers with Embedded PC technology 3-1 All TDAT mass spectrometers 3-1 AutoSpec Premier 3-1 ZQ Mass Detector 3-1 Quattro Micro API 3-2 Quattro Micro GC 3-2 Quattro Premier, Quattro Premier XE 3-2 Quattro Ultima 3-3 Quattro Ultima Pt 3-3 QuattroLC EPCAS 3-3 LCT Premier 3-4 LCT 3-4 MALDI micro MX 3-4 Q-Tof (generic) 3-4 Q-Tof Premier 3-4 Q-Tof API 3-4 MassLynx 4.1 Release Notes 716001833 / A vii

Q-Tof Global 3-5 Q-Tof Micro 3-5 Inlet Enhancements and... 3-6 Overall new features and enhancements 3-6 ACQUITY 3-6 CTC_HTS_PAL 3-6 CTC Combi PAL 3-6 Agilent/HP 1100 3-6 HP 6890 3-7 Jasco 3-7 Waters 1525 Binary HPLC pump 3-7 Waters 2525 Binary Gradient Module and Column Fluidics Organizer 3-7 Waters 2690/2695 Separations Module 3-7 Waters 2747/2767 Sample Manager 3-7 Waters 2777 Sample Manager/CTC HTS PAL 3-7 Waters 2790/2795 Separations Module 3-8 Waters 515 HPLC Pump 3-8 Waters 600 HPLC Pump 3-8 Waters 2420 Evaporative Light Scattering Detector (ELSD) 3-8 Software application enhancements and fault fixes... 3-9 Accurate Mass 3-9 All File Accurate Mass Measurement ( AFAMM ) 3-9 AutoLynx 3-9 AutoPurify 3-9 BackLynx 3-10 ChromaLynx 3-10 Chromatogram 3-10 Data-directed acquisition (DDA) tool 3-10 Elemental composition 3-11 FractionLynx and AutoPurify 3-11 FractionLynx browser 3-12 Help 3-12 Library 3-12 LogLynx 3-12 MALDI PSD 3-12 MarkerLynx 3-13 MassLynx Top Level 3-13 MetaboLynx setup and processing 3-14 MetaboLynx browser 3-15 NeoLynx 3-15 viii 716001833 / A MassLynx 4.1 Release Notes

OpenLynx 3-15 OpenLynx browser 3-16 OpenLynx Open Access Login 3-16 OpenLynx Toolkit 3-17 Printing 3-17 ProfileLynx 3-17 Quan Optimize 3-17 QuanLynx 3-17 Waters NuGenesis Scientific Data Management System (SDMS) 3-18 MassLynx Security 3-18 Shutdown 3-19 Spectrum 3-19 Strip 3-19 TargetLynx 3-20 4 MassLynx 4.1 Software Notes...4-1 Mass spectrometer control notes... 4-1 All Mass Spectrometers 4-1 All Quadrupole Mass Spectrometers 4-1 All MS with ESCI 4-1 AutoTune for quadrupole mass spectrometers (ZQ, Quattro micro, Quattro Premier, Quattro Premier XE) 4-1 AutSpec 4-2 LCT 4-2 LCT Premier 4-2 M@LDI 4-4 MALDI Micro MX 4-4 Q-Tof Ultima API, Q-Tof API-US 4-4 Q-Tof Micro 4-5 Q-Tof Premier 4-5 Quattro micro 4-9 Quattro Micro GC 4-9 Quattro Premier 4-9 Quattro Ultima 4-9 ZQ 4-9 Inlet control notes... 4-10 General information 4-10 ACQUITY 4-10 Gilson 4-10 HP 1100 4-11 HP 6890 4-11 MassLynx 4.1 Release Notes 716001833 / A ix

Shimadzu (autosampler) 4-11 Waters 1525 4-11 Waters 2777/CTC HTS PAL 4-11 Waters 2795 Separations Module 4-11 Waters 2420 Evaporative Light Scattering Detector (ELSD) 4-11 Waters SAT/IN 4-12 MassLynx software and application manager notes... 4-13 Accurate Mass 4-13 ChromaLynx 4-13 DataBridge 4-13 FractionLynx 4-13 Installation 4-14 MetaboLynx 4-14 NeoLynx 4-14 Quan Optimize 4-14 QuanLynx 4-14 MassLynx Full Security 4-14 Spectrum 4-14 Startup and Shutdown 4-15 TargetLynx 4-15 x 716001833 / A MassLynx 4.1 Release Notes

1 General Information Note: TGR numbers appear throughout this document following the listing of certain items. Waters assigns these numbers and uses them internally to track the status of issues associated with MassLynx software. MassLynx 4.1 is a single-system software product designed to control a variety of Waters/Micromass mass spectrometers. It does not run simultaneously with Waters Millennium, Breeze, or Empower chromatography manager software. To successfully communicate with the ZQ mass spectrometer from a workstation on which both MassLynx and Empower (or Millennium) are installed, you must reboot the mass spectrometer's embedded PC each time you switch from one application to the other. Micromass mass spectrometers supported ZQ ZMD Quattro micro API Quattro micro GC Quattro Premier Quattro Premier XE Quattro Ultima Quattro Ultima Pt Quattro LC (T-DAT and EPCAS) AutoSpec AutoSpec Premier Q-Tof Premier LCT Premier LCT Q-Tof micro Q-Tof Ultima API Q-Tof API-US Q-Tof Ultima Global MALDI micro MXM@LDI family MassLynx 4.1 Release Notes 716001833 / A 1-1

Q-Tof II EPCAS (only) Micromass mass spectrometers not supported Quattro I Quattro II BioQ Platform Series Q-Tof I Q-Tof I EPCAS Upgrade Q-Tof II T-DAT Q-Tof Ultima MALDI TofSPEC GCT GCT Premier Micromass mass spectrometers supported Full Security installations ZQ Quattro Premier Quattro Premier XE Quattro micro API Quattro micro GC Quattro Ultima Pt Quattro Ultima Quattro LC LCT Premier LCT Q-Tof Premier Q-Tof micro Q-Tof API, Q-Tof API (US) Q-Tof II MassLynx application managers supported in Full Security installations QuanLynx TargetLynx 1-2 716001833 / A MassLynx 4.1 Release Notes

Operating HPLC Instruments controlled by the National Instruments GPIB controller board (part number 186000825) Use NI-488.2 for Windows version 2.1 (Windows 2000 or Windows XP). NI-488,2 is on the MassLynx 4.1 CD2, in the GPIB V 2.1 folder. Waters inlets instrument support information This table presents minimum firmware requirements for the Waters components that MassLynx 4.1 supports: Product 996 PDA detector 1.8 Minimum firmware requirements Minimum Version verification version Revision displayed on the CPU board. (1.8 EPROM) Upgrade part number N/A 2996 PDA detector 3.5 N/A (no other versions available) (no other versions available) W2487 UV detector 1.02 Revision displayed in the detector s diagnostics and in the System Information window. Performed at no charge by a Waters Service Engineer W2488 MUX UV detector Waters 2420 ELSD detector 2.01 Revision displayed in the detector s diagnostics and in the System Information window. 1.0 Revision displayed in the detector s diagnostics and in the System Information window. Part number 361000213 N/A bussat/in 20.0 Label on the PCB WAT200415 (bussat/in Module) Alliance 2690/2695 separations module 2796 bioalliance 2790/2795 separations module 2.03 Displayed at power-on 667000509EN 2.1 Displayed at power-on N/A MassLynx 4.1 Release Notes 716001833 / A 1-3

Product Minimum firmware requirements Minimum version Version verification Upgrade part number Alliance 2796 bioseparations module 2.1 Displayed at power-on N/A 515 pump 1.0 Displayed at power-on N/A Pump control module 2.2 N/A N/A (no other versions available) Pump control module II 3.0 N/A N/A 1525 pump 1.3 N/A (no other version available) N/A (no other version available) 1525µ pump, 1525EF pump 2.01 or 2.02 N/A (no other version available) N/A (no other versions available) 600 pump 4.2 Displayed at power-on 2700 sample manager All CapLC All Delta Prep 4000 3.1 Delta Prep 2000 3.1 2525 binary gradient pump 1.08 Part number 361000215 C/FO 1.05 N/A 2767 sample manager All N/A (no other version available) (no other version available) 1-4 716001833 / A MassLynx 4.1 Release Notes

Product Minimum firmware requirements Minimum version Version verification Upgrade part number 2747 sample manager All N/A (no other version available) 2777 sample manager 2.4.0 2.4.0 (as displayed on Handheld Controller, service-only install) WFC II/WFC III ACQUITY binary solvent manager All 1.20 Displayed in ACQUITY Console. Select "View Module Info" ACQUITY sample manager (autosampler 1.20 Displayed in ACQUITY Console. Select "View Module Info" ACQUITY TUV detector 1,20 Displayed in ACQUITY Console. Select View Module Info ACQUITY Sample Organizer 1,20 Displayed in ACQUITY Console. Select View Module Info ACQUITY 2996 PDA detector; ACQUITY UPLC TUV Detector ACQUITY UPLC 2996 detector 1.10 4.10 Displayed in ACQUITY Console. Select View Module Info MassLynx 4.1 Release Notes 716001833 / A 1-5

Product ACQUITY ELSD detector Minimum firmware requirements Minimum version Version verification 1.20 Displayed in ACQUITY Console. Select View Module Info Upgrade part number ACQUITY ELSD Detector N/A Will be specified on release of ACQUITY ELS Detector Unsupported Waters inlets MassLynx 4.1 does not control the following instruments and devices. However, you may nevertheless include them in HPLC systems: Waters 1515 pump Waters 717 Autoinjector Waters 2410 RI Detector Waters 2414 RI Detector Waters 474 Fluorescence Detector Waters 2465 Electrochemical Detector Waters 2475 Fluorescence Detector Waters 484 Tunable UV Detector Waters 486 Tunable Absorbance Detector Waters 470 Scanning Fluorescence Detector Waters 460 Electrochemical Detector Waters 464 Pulsed Electrochemical Detector Waters 430, 431, and 432 conductivity detectors Analog detector data may be collected through a Waters SAT/IN Module or one of the analog inputs on the mass spectrometer. Analog data collection using the Waters SAT/IN Module is not supported in UVonly systems (that is, systems with no mass spectrometer) unless an IEEE-488 detector (Waters 2487 or Waters 996) is also configured (PCS # 11710). 1-6 716001833 / A MassLynx 4.1 Release Notes

Non-Waters inlets instrument support information Agilent /HP system Supported G1310A* G1311A quaternary pump* G1312A binary pump* G1313A Auto-sampler G1314A VWD G1315A DAD detector * G1315B DAD detector * G1316A column heater G1323A HPLC controller G1326A HPLC controller G1327A autosampler G1329A thermostatic autosampler G1330A Thermostatic Autosampler) G1368A Agilent 1100 Well plate autosampler (includes. thermostatic option) G1367 microtitre plate autosampler G1389A MicroALS autosampler includes thermostatic option G1376A capillary HPLC pump G1379A de-gasser Supported Firmware Standard Agilent 1100 systems (w/ G1323A Control module) A.05.01, A.04.11, A.04.06, A.03.81, A.03.60, A.03.32, A.03.50 A.05.01, A.04.11, A.04.06, A.03.81, A.03.60, A.03.32, A.03.50 A.05.01, A.04.11, A.04.06, A.03.81, A.03.60, A.03.32, A.03.50 A.05.04 A.05.01, A.04.10, A.04.06, A.03.80, A.03.61, A.03.30, A.03.31 A.05.01, A.04.10, A.04.06, A.03.80, A.03.60, A.03.30 A.05.01, A.04.11, A.04.06, A.03.80, A.03.61, A.03.30 A.04.11, A.04.06, A.03.80, A.03.61, A.03.30 A.05.01, A.04.11, A.04.06, A.03.80, A.03.90, A.03.60, A.03.30 A.02.10, A.02.02 Firmware version not available /verified Firmware version not available /verified 5.01, A.04.10, A.04.06, A.03.61, A.03.80x, A.03.61, A.03.30, A.03.31 Firmware version not available /verified A.04.08 A.05.04 A.04.06 A.05.04 A.04.08 Firmware version not available /verified MassLynx 4.1 Release Notes 716001833 / A 1-7

* Standard HP1100 modules fitted with the following main electronic boards accept only A.04.xx revision firmware: G1310A, with main board G1311-66530 G1311A, with main board G1311-66530 G1312A, with main board G1312-66530 G1315, with main board G1315-66530 HP GC system GC HP6890 HP6890N Firmware A.05.04,05.05 N.05.04 Autosampler AS800 HP6890 HP7683 with/without the DICE option Gilson system HPLC Autosampler UV Detectors 305 222 118 306 231 307 232 321 Nebula FW Version1.02 233 322 Nebula 215 (FW Version 2.20) JASCO system QuadZ-215 (FW Version 1.7) HPLC Firmware Autosampler Firmware JASCO 900 2.56 JASCO 1500 2.15 JASCO 1580 1.14 1-8 716001833 / A MassLynx 4.1 Release Notes

JASCO system (continued) Column Oven Firmware UV Detectors Firmware CO-1560 N/A 1575 UV 1.12 LCNet II box firmware version, v4.22 is supported; V4.24 is not supported. UltiMate LC Packing system Pump Firmware Autosampler Firmware Ultimate 5.09, 6.00 FAMOS Well Plate 2.04, 2.03 FAMOS Carousel 1.14 Secondary Firmware UV Detectors Firmware SWITCHOS 2 5.09, 6.0 Ultimate 1.05, 1.54 Shimadzu system HPLC Firmware Autosampler Firmware Column Oven LC- 10ADvp 5.27 SIL-10ADvp 5.32 CTO- 10ASvp LC-10AD N/A SIL-10A N/A CTO- 10Avp* LC- 10ATvp N/A SIL-10Ai N/A CTO- 10ACvp* LC-10AT N/A SIL-10Axl N/A CTO- 10A* LC-10AS N/A SIL-HTc 6.03 CTO- 10AC* LC-10Ai N/A SIL-HTa 6.03 LC-8A LC-7A LC-6AD N/A N/A N/A Firmware 5.24 N/A N/A N/A N/A MassLynx 4.1 Release Notes 716001833 / A 1-9

Shimadzu system (continued) System Controller SCL- 10Avp Firmware Fraction Collector Firmware Detectors Firmware 5.42 FRC-10A N/A APD-10Avp N/A SPD- 10AVvp SPD- 10Avp* SPD-10A* SPD-10AV* 5.23 N/A N/A N/A N/A Firmware version not available /verified CTC Pal system Autosampler CTC Combi PAL (Cycle Composer V1.4 required) CTC GCPAL CTC A200S/SE Firmware N/A N/A N/A CTC HTS PAL 2.2.4, 2.4.0 CTC HTS PAL Harney Valve 4 way injection supported N/A Firmware version not available /verified 2.2.4,2.4.0 1-10 716001833 / A MassLynx 4.1 Release Notes

Minimum computer hardware configurations Single Quadrupole Mass Spectrometers (Waters ZQ and ZMD Detectors) and the Quattro micro Mass Spectrometer: Compaq EVO 510 512 MB RAM 20 GB ATA hard drive, 80 GB recommended 1.44 MB floppy drive, 3-1/2 inch CD/RW drive 17-inch monitor SVGA Microsoft serial mouse Embedded Ethernet controller Auxiliary Intel Pro 100+ Network NIC NVIDIA Riva AGP2x Graphics Card Embedded Audio and Integrated Premier Sound Printer supported by Windows NT NTFS All other Waters/Micromass Mass Spectrometers IBM IntelliStation MPro 2.2 GHz (also suitable for use with ZQ and Quattro micro instruments) 512 MB 73.4 GB Ultra160 SCSI hard drive 1.44 MB floppy drive, 3 ½ inch CD/RW drive 17 inch monitor Microsoft Serial Mouse Embedded Ethernet controller Auxiliary Intel Pro 100+ Network NIC Matrox Millennium G450 video card Printer supported by Windows NT NT file system ( NTFS) Tip: Waters strongly recommends the IBM ThinkCENTRE M50 or M51 for MassLynx Acquisition Workstations: MassLynx 4.1 Release Notes 716001833 / A 1-11

IBM ThinkCENTRE M50 Pentium 4, 3.0 GHz/800 MHz FSB, 512 KB Cache IBM 1024 MB SDRAM Pro keyboard Optical 3-Button ScrollPoint Mouse PS2 and USB 160 GB 7200 RPM (Serial ATA-150 hard drive) DVD Multi-Burner Roxio Multi Burner software Windows XP Professional Intel Extreme Graphics 2 Direct AGP 32 MB Graphics Chipset IBM M51 ThinkCentre Pentium 4, 3.2 GHz/800MHz FSB, 1 MB Cache IBM 1024 MB SDRAM Pro Keyboard Optical 3-Button ScrollPoint Mouse PS2 and USB 160 GB 7200 RPM (Serial ATA-150 hard drive) DVD Multi-Burner Roxio Easy CD Creator & DVD Creator 6 Com 2 Cable Windows XP Professional Minimum Computer Hardware Configuration for MassLynx 4.1 for Systems Equipped with MUX Multi-Inlet Systems (Analytical MUX or Purification Factory Systems) IBM Z-PRO Dual XEON Processor IntelliStation Dual XEON Processors, 2.4 GHz 512 MB RAM 36.4 GB SCSI HHD 120 GB 7200 RPM ATA/100 EIDE HDD IBM DVD Multi Burner IBM keyboard/mouse PRO 10/100/1000 MT PCI Fast Ethernet controller Matrox Graphics Card, Dual video mode disabled 17-inch LCD-flat panel monitor NTFS 1-12 716001833 / A MassLynx 4.1 Release Notes

Tip: Waters strongly recommends the IBM M Pro IntelliStation for systems equipped with MUX Inlets: IBM M Pro Intellistation Pentium 4, 3.2 GHz processor with hyperthreading technology 800MHz Front Side Bus 512 KB Cache IBM 2 x 512MB DDR-PC2700 (4 GB maximum memory capacity) (dual channel memory) IBM 1024 MB SDRAM Pro Keyboard Optical USB Wheelmouse 80 GB and 160GB 7200RPM (Serial ATA-150 hard drive NVIDIA Quadro FX 1100, 128MBand AGP 8X with dual monitor support DVD Multi-Burner IV Windows XP Professional Roxio Easy CD & DVD Creator v6 (not installed) Intel Pro 1000 MT Desktop Adapter MassLynx 4.1 Release Notes 716001833 / A 1-13

Supported operating systems Microsoft Windows 2000 with Service Pack 4 (Note that only the English (United States) version of the operating system is supported.) Microsoft Windows XP Professional with Service Pack 2. The Windows XP Firewall should be disabled on the dedicated instrument LAN (Note that only the English (United States) version of the operating system is supported.) Microsoft Security hot fixes tested with MassLynx 4.1: Windows Updates For Windows XP SP2 MS05-009 - KB887472 - Windows Media Player 9 Series MS05-016 - KB893086 MS05-018 - KB890859 MS05-019 - KB893066 V2 MS05-020 - KB890923 for IE 6.0 SP1 MS05-026 - KB896358 MS05-027 - KB896422 MS05-032 - KB890046 MS05-033 - KB896428 MS05-036 - KB901214 MS05-038 - KB896727 for IE 6.0 SP1 MS05-039 - KB899588 MS05-040 - KB893756 MS05-041 - KB899591 MS05-042 - KB899587 MS05-043 - KB896423 Host Process error update - KB894391e Windows Installer v3.1 - KB893803 Package Installer v6.1.22.4 - KB898461 Step by Step Interactive Training - KB898458 NET Framework SP1 - KB867460 MS05-004 - NET Framework SP1 Update - KB886903 Windows Malicious Software Removal Tool for v1.7.1 - KB890830 Windows Updates For Windows 2000 SP4 Update Rollup 1 for Windows 2000 SP4 KB891861 1-14 716001833 / A MassLynx 4.1 Release Notes

MSXML 4.0 Windows Updates For Windows 2000 SP4 KB828026 Windows Media Player script commands KB842773 Background Intelligent Transfer Service (BITS) 2.0 MS02-050 KB329115 MS04-028 KB833989 for IE 6.0 SP1 MS05-009 - KB885492 - Windows Media Player 9 Series MS05-016 - KB893086 MS05-018 - KB890859 MS05-020 - KB890923 for IE 6.0 SP1 MS05-024 - KB894320 MS05-026 - KB896358 MS05-027 - KB896422 MS05-030 - KB897715 for Outlook Express 6.0 SP1 MS05-032 - KB890046 MS05-033 - KB896428 MS05-036 - KB901214 MS05-038 - KB896727 for IE 6.0 SP1 MS05-039 - KB899588 MS05-040 - KB893756 MS05-042 - KB899587 MS05-043 - KB896423 Host Process Error update - KB894391 Windows Installer v3.1 - KB893803 Windows Step-by-Step Interactive Training - KB898458 NET Framework SP1 - KB867460 MS05-004 -.NET Framework SP1 update - KB886903 Malicious SW Removal Tool for Windows v1.7.1 - KB890830 Cumulative Security Update for Internet Explorer for Windows XP (KB896688) has not been tested by Waters. Installation is not supported at this time. PC power settings, hyperthreading, third-party application compatibility, and peripherals. PC Power Settings, Hyperthreading, Third-Party Application Compatibility, and Periphera ls To operate MassLynx reliably, you must disable BIOS and the Operating System Power Saving features. For PCs that support it, hyperthreading should remain enabled when running Windows XP. However, if Windows 2000 is the operating system, disable hyperthreading, in the BIOS. MassLynx 4.1 Release Notes 716001833 / A 1-15

Serial interface control card Waters strongly recommends using the Edge Port USB to Serial Converter in systems where an Equinox card is currently used. Antivirus software- MassLynx 4.1 supports operating with real-time virus protection software. MassLynx 4.1 was tested with antivirus clients operating with File System Realtime Protection feature enabled. Note that MassLynx does not support acquiring data while running a full system antivirus scan. You must therefore initiate full system virus scans only when MassLynx acquisition is idle,; ensure that scheduled antivirus scans do not initiate when MassLynx will be acquiring data. The minimum supported version of McAfee antivirus software is McAfee Virus Scan Professional 2004, version 8.0 (PCS # TG401). If you use this product, you should clear the Enable Script Stopper option in the Advanced window of the McAfee Configure Virus Scan Options (PCS # 11850). 1-16 716001833 / A MassLynx 4.1 Release Notes

2 Installing MassLynx 4.1 You must install MassLynx 4.1 on a drive formatted for the NTFS file system. It cannot be installed on a FAT-formatted drive. The installation directory must be the folder C:\MassLynx. Do not move the folder once it is created. You must uninstall any existing MassLynx installation and any installed Waters instrument control software before installing MassLynx 4.1. General installation procedure 1. Restart the MassLynx workstation. 2. Uninstall Waters instruments software using the Control Panel's Add/Remove utility. 3. Uninstall MassLynx 4.0 procedure, using the Control Panel's Add/Remove utility. 4. Insert the MassLynx 4.1 installation CD (CD1) into the CD-ROM drive. 5. If Autorun fails to run, from the Windows taskbar, select Start > Run. 6. In the Run dialog box, type drive: \SETUP, replacing drive with the letter that represents your CD-ROM drive. 7. Click the OK button. 8. Follow the steps outlined in the wizard to install MassLynx 4.1. 9. When the installation is complete, remove MassLynx 4.1 CD1, and insert MassLynx 4.1 CD2. 10. Browse to and open the Black Box folder, and then run AppSight Black Box.exe. 11. For systems using mass spectrometers with embedded PC subsystems, reboot the embedded PC. 12. Wait at least 4 minutes before starting MassLynx Installing MassLynx 4.1 with Waters inlets controlled by Ethernet 1. Power-off all Ethernet instruments. 2. Install MassLynx 4.1, following the procedure above. 3. Right click on My Network Places and choose Properties. In the Network Places Properties dialog box, set the IP addresses for the mass spectrometer and any Waters instruments controlled by Ethernet devices. MassLynx 4.1 Release Notes 716001833 / A 2-1

4. Requirement: The Waters instruments' IP address (192.168.0.1) must appear first on the list. The mass spectrometer's IP address (64.1.1.1) must appear second. 5. Rule: List order is especially important for UV-directed systems because the basic PC image from the factory defines the MS IP address. 6. If required to do so, define the printer as either local or network. 7. For systems using mass spectrometers with embedded PC subsystems, reboot the embedded PC. 8. Wait at least 4 minutes before starting MassLynx. 9. Start up MassLynx. If there is a Mass Spectrometer installed, check that the Mass Spectrometer is present in the MassLynx Toolbar. 10. Open the Inlet Editor, and configure the inlet system. 11. In the list of Pumps, either choose Waters ACQUITY or Waters Pump Control (Waters 2525, W600, 1525, 515), or Waters 2796. 12. Choose Autosampler from list. 13. Choose detector(s) from list. 14. Exit the Inlet Wizard. 15. Let the Waters Instrument Control Operating Pack (ICOP) run. Select the instruments you configured. When the ICOP installation has completed, exit MassLynx and reboot the PC. 16. When the PC is operational, power on the Ethernet instruments and wait for them to initialize. 17. Start MassLynx. 18. For Waters Pump Control or Waters 2796 Inlets, open the Inlet Editor. The Modify Instrument Method dialog will open. Click on the W icon in the top left hand corner and select Configure Autopurification Modules from the drop down list. 19. In the Autopurification System Configuration dialog, Scan for the Waters instruments. 20. Close and restart MassLynx to reset the Additional Status page. 21. Close and then restart MassLynx to reset the Additional Status page. Installing MassLynx 4.1 and OALogin Requirement: You must remove any previous version of OALogin. Rule: Previous versions of OALogin are not compatible with MassLynx 4.1. 1. Ensure the key disk is available before initiating installation. 2. Insert the MassLynx 4.1 CD2 into the CD-ROM drive. 3. From the Windows taskbar, select Start > Run. 2-2 716001833 / A MassLynx 4.1 Release Notes

4. In the Run dialog box, enter drive:\oalogin\setup, replacing drive with the letter that represents your CD-ROM drive. 5. Click OK. 6. For systems using mass spectrometers with embedded PC subsystems, reboot the embedded PC. 7. Wait at least 4 minutes before starting MassLynx. MassLynx 4.1 Release Notes 716001833 / A 2-3

3 New Features and in MassLynx 4.1 A brief summary of MassLynx 4.1 enhancements and major faults follows, organized by mass spectrometer, inlet, and application manager. Note that TI numbers provide traceability for customer-reported faults. TGR numbers are for Waters' internal use as software change tracking numbers. Mass Spectrometer Enhancements and. Enhancements are described following the heading. are labeled. Mass Spectrometer Enhancements and All mass spectrometers with Embedded PC technology A warning message appears whenever you attempt to close the Tune page during data acquisition. A warning message appears whenever you attempt to start a sample queue while the instrument in standby mode. All TDAT mass spectrometers TDAT mass spectrometers are supported with PCI TDAT cards only. AutoSpec Premier The AutoSpec Premier is supported in V4.1 rather than on a software change note (SCN). ZQ Mass Detector A series of wizards drive AutoTune, mass calibration, and creation of SIR methods. Results can be reported using a reporting tool. The inter-channel delay and span values are reported from the raw data file experimental record (TI 15475, TGR 183). The Method Experiment report printout shows inter-channel delay and span (TI 15475, TGR 182). The cone gas control ranges are configurable for instrument hardware type (TI 19107, TGR 1779). The calibration scan speed compensation reports the scan speed correctly. Previous versions of MassLynx used the cycle time, rather than the scan time, to calculate the scan speed (TGR 3420). MassLynx 4.1 Release Notes 716001833 / A 3-1

Quattro Micro API A series of wizards drive AutoTune, mass calibration, and SIR and MRM method creation. Results can be reported using a reporting tool. Collision energy ramping operates for MS2 in daughter acquisitions (TI 15245, TGR 121). The method editor range checks the start mass/set mass for neutral loss (TI 15192, TGR 264). The software correctly verifies calibration for MS2 when performing calibrate and verify (TI 14452, TI 14923, and TGR 211). Neutral loss acquisitions are calibrated (TI 18433, TGR 525) When rebooting the EPC via telnet > reboot or resetting communications from the Tune page, the collision gas state is set to the correct state (TI 19425, TGR 701). The Inter-channel Delay and Span are missing from the raw data file experimental record. (TI 15475, TGR 183). Method Experiment Report printout does not show inter-channel delay and span (TI 15475, TGR 182). The cone gas control ranges are configurable for the instrument hardware type (TI 19107, TGR 1779). The calibration scan speed compensation reports the scan speed correctly. Previous versions of MassLynx used the cycle time, rather than the scan time, to calculate the scan speed (TGR 3420). Quattro Micro GC Quattro Micro GC is supported in V4.1 rather than on a software change note. The Method Editor range checks the start mass/set mass for neutral loss (TI 15192, TGR 264). Readbacks are correct at all scan speeds (TI 21377, TGR 2002). DCI probe ramp operation limited to1500ma to be applied. (TI 23356, TGR 3091). The calibration scan speed compensation reports the scan speed correctly. Previous versions of MassLynx used the cycle time, rather than the scan time, to calculate the scan speed (TGR 3420). Quattro Premier, Quattro Premier XE A series of wizards drive AutoTune, mass calibration, and SIR and MRM method creation. Results can be reported using a reporting tool. 3-2 716001833 / A MassLynx 4.1 Release Notes

The Method Editor range checks the start mass/set mass for neutral loss (TI 15192, TGR 264). Neutral-loss acquisitions are calibrated (TI 18433, TGR 525). The calibration scan speed compensation reports the scan speed correctly. Previous versions of MassLynx used the cycle time, rather than the scan time, to calculate the scan speed (TGR 3420). Quattro Ultima The sample list operates correctly with event out (TI 15676, TGR 136). The calibration scan speed compensation reports the scan speed correctly. Previous versions of MassLynx used the cycle time, rather than the scan time, to calculate the scan speed (TGR 3420). Quattro Ultima Pt The sample list operates correctly with event out (TI 15676, TGR 136). The Tune page closes or crashes when you attempt acquisitions of more then 12 SIR functions (TI 13372 TGR 497). The method editor range checks the start mass/set mass for neutral loss (TI 15192, TGR 264). Neutral-loss acquisitions are calibrated (TI 18433, TGR 525) The calibration scan speed compensation reports the scan speed correctly. Previous versions of MassLynx used the cycle time, rather than the scan time, to calculate the scan speed (TGR 3420). QuattroLC EPCAS The Tune page closes or crashes when you attempt acquisitions of more then 12 SIR functions (TI 13372 TGR 497). The software correctly verifies calibration for MS2 when performing the calibrate and verify operations. (TI 14452, TI 14923, TGR 211) Neutral-loss acquisitions are calibrated (TI 18433, TGR 525). The calibration scan speed compensation reports the scan speed correctly. Previous versions of MassLynx used the cycle time, rather than the scan time, to calculate the scan speed (TGR 3420). MassLynx 4.1 Release Notes 716001833 / A 3-3

LCT Premier Wizards automatically set up the LCT Premier for accurate mass and indicate when the instrument will not achieve accurate mass. DRE settings are stored on a per optic/polarity mode basis. Aperture 1 can be switched on a per function basis. The inter scan delay is set automatically. The peak display can show resolution reading or ions per push. When calibrating from a file, pusher cycle time and mass range are recorded correctly (TI 21693, TGR 458). Redundant TDC edge control and gain settings are removed (TI 21702, TGR 2196). Analog Data is recorded for the full length of the sample acquisition (TGR 2974). LCT Redundant TDC edge control and gain settings are removed. (TI 21702, TGR 2196). MALDI micro MX The MALDI Micro MX is supported in V4.1 rather than on a software change note (SCN). Q-Tof (generic) Redundant TDC edge control and gain settings are removed (TI 21702, TGR 2196). Q-Tof Premier Q-Tof API The Q-Tof Premier is supported in V4.1 rather than on a software change note (SCN). MALDI source is supported in v4.1. Wizards automatically set up the Q-Tof Premier for accurate mass. The wizards are optimized for operation with the Lock Spray source and small molecule type applications, and they indicate when the instrument fails to achieve accurate mass. Improved Elemental Composition calculations (i-fit Algorithm) are available for Q-Tof Premier 3-4 716001833 / A MassLynx 4.1 Release Notes

Q-Tof Global EPC reboots if vacuum gauges are requested during acquisition with TTP TDC (TGR 1657). Instruments fitted with TTP 4GHz TDC cards maintain configuration setting (TI 20475, TGR 1666). Instruments fitted with TTP 4GHz TDC cards maintain configuration setting (TI 20475, TGR 1666). Q-Tof Micro Reference spray utilizes the correct CE, not the CE for the last-run parent function (TI 17865, TGR 884). Reference spray scan time remains constant for all scans (TI 17865, TGR 885). Experimental header data is reported correctly for DDA experiments (TI 17865, TGR 886). Multi function experiments support different MSMS collision energy profiles (TI 17865, TGR 887). MassLynx 4.1 Release Notes 716001833 / A 3-5

Inlet Enhancements and Overall new features and enhancements ACQUITY All Waters pumps (1525, 2525, W600, 515 with PCM) are controlled through Waters Pump Control software. MassLynx 4.1 provides an inlet event log. All Waters and Agilent PDA, UV and ELSD detectors are supported for network acquisitions in all modes of operation. Detectors support 20Hz data rates. nanoacquity is supported in v4.1 without a software change note (SCN). ACQUITY Data Channels are supported as analog channels on v4.1 CTC_HTS_PAL (See Waters 2777/CTC HTS.) CTC Combi PAL SPME and Headspace GC/MS methods are supported in 4.1. Agilent/HP 1100 HPLCFile includes a gradient override that can be applied to a prerun or main run. HPLCFile includes the ABCD % composition to override the mobile phase parameters of pre run. Override Inlet method file switch patterns with HPLC file switch parameters. The column name and the switch pattern are included in the experiment information. The HP 1100 G1367a Well Plate Autosampler supports user-generated plates (TGR 3). Oven temp no longer reported in experimental record when oven is switched off (TI 2237, TGR 3053). Agilent 1100 UV operates with 2700 sampler (TI 15899, TGR 155). Agilent/HP 1090 TI 15298 TGR 146 WashOn feature is reinstated for the Agilent 1090 autosampler. 3-6 716001833 / A MassLynx 4.1 Release Notes

Jasco MassLynx 4.1 supports control of JASCO devices with LC NET II box. HP 6890 HP 6890N GC with a 7683 autosampler injects correct volume (TI 17534, TGR 535). Injection Volume is reported correctly in the Experiment file (TI 19852, TGR 759). Three-minute run time restriction with JASCO autosampler has been removed in time (TI 18881 TGR 630). Waters 1525 Binary HPLC pump Instrument control is only via Waters Pump Control software. Experimental Record for staggered chromatography includes HPLC conditions for all samples (TI 21128, TGR 1956). Waters 2525 Binary Gradient Module and Column Fluidics Organizer Instrument control is only via Waters Pump Control software. Waters 2690/2695 Separations Module The column name and the switch pattern are stored as experiment information. Inlet report provides correct loop purge volume for 2690/2695(TI 17652 TGR 476). Waters 2747/2767 Sample Manager Configuration dialog supports 25-mL syringe. Fraction mixing is supported. Multiple sample draws per injection are supported. Instrument supports 20-mL and 25-mL sample loop options. Sample sandwiching control is supported. Waters 2777 Sample Manager/CTC HTS PAL The ctcsngid.exe driver supercedes paldriv.exe to support operation in the MassLynx Full Security mode. MassLynx 4.1 Release Notes 716001833 / A 3-7

An option of Alpha-numeric referencing for CTC/Waters 2777 autosampler. The Experimental Record for Staggered Chromatography includes LC conditions for all samples (TI 21128, TGR 1956) Instrument operates with project-switching Waters 2790/2795 Separations Module The column name and the switch pattern are stored in the experiment information. Column-switching events for the Waters 2695 Separations Module are processed correctly (TI 16943 TGR 348). Waters 515 HPLC Pump Device control is only via Waters Pump Control software. Waters 600 HPLC Pump Operation of the Pump control module (PCM) is via the Waters Pump Control software only. Waters 2420 Evaporative Light Scattering Detector (ELSD) Waters 2420 ELSD operates in systems configured with a Waters SAT/IN module. Waters 2420 ELSD operates in Network Acquisitions with full security. Waters 2420 ELSD operates with analog channels from the MS. 3-8 716001833 / A MassLynx 4.1 Release Notes

Software application enhancements and fault fixes Accurate Mass Lock mass correction for accurate mass Data smoothing, so that smooth width is appropriate to peak width across a mass range Adaptive background subtract for accurate mass post-processing Automatic Peak detection for Accurate Mass Dead-time correction for Accurate Mass All File Accurate Mass Measurement ( AFAMM ) AutoLynx AutoPurify Supports automatic peak detection parameters for accurate mass. Supports continuous lock mass correction for continuum data. Printing from FractionLynx report files (FPT) files via AutoLynx. Allow selection of Minimum Intensity Threshold (MIT) file per narrow and generic method. Allow selection of MIT file on Walkup page for use with Open Access FractionLynx. Report Collected Volumes in FractionLynx report files (FPT) file. An option to select best tube using intensity of targets. Select pool indices using intensity of targets. An option to group fractions separated by a small time in tube selection and pooling. Check the RT and % total area for a specified set of chromatograms. Allow user to monitor at least 5 peaks in QC. Allow separate processing parameters for MS positive and MS negative data. Perform QC Intensity test on multiple masses. Improved mixed trigger support in AutoPurify preparative stage OLB generation Sample Purity not generated for Mass Target and UV Wav trace (TI 17183, TGR 463).. Waste is treated as a peak when fraction trigger times are used for combine times (TI 18832 TGR 643). MassLynx 4.1 Release Notes 716001833 / A 3-9

BackLynx Provides an "older than" field to select data for backup. ChromaLynx Improved peak detection for ChromaLynx Identify. Lets you remove components from a ChromaLynx Identify data set. Add multiple functions to ChromaLynx Identify Enable multi-function screening of samples in ChromaLynx Convert MassLynx <-> NIST libraries, retaining filter information Enable filtering of library results in ChromaLynx Update ChromaLynx to link & process components across functions and calculate average match Export Clinical Screening candidate information Fault Fixes Comparing more than two samples can crash ChromaLynx Compare Saving MultipleSamples.ids file causes browser to crash Chromatogram Chrotool Utility lets you automatically initialize the chromatogram view using pre-saved chromatograms. Chrotool Utility lets you automatically initialize the chromatogram view. You can specify range when launching a group of chromatograms. MassLynx reports data from ELSD detectors as LSU units. Chromatogram can display multiple trace chromatograms. Detector traces are available on chromatogram copy list. A fraction prediction tool lets you determine trigger parameters without injecting a sample. Data-directed acquisition (DDA) tool Additional ion characteristics displayed DDA reporting is improved. DRE operates on MSMS data during DDA. Display the Table of Precursor Ions. Display characteristics of ions. Display MS and MS/MS data per ion. Initiate an ion list from Chromatogram Application. 3-10 716001833 / A MassLynx 4.1 Release Notes

Show MS and MS/MS data for one precursor at a time. DDA collision energies set correctly (TI 19455, TGR 2944) Elemental composition An isotopic model of each elemental composition is evaluated statistically. The list of elemental compositions is truncated based on the isotope fit (i-fit algorithm). Nitrogen valency rules are applied. C13 ratio is applied. Isotope pattern matching filters for carbon, halogens, and sulfur are supported. FractionLynx and AutoPurify Fraction simulation feature, accessed through the Chromatogram window, lets you determine optimal trigger parameters without injecting a sample Sample list spare fields are reportable in FractionLynx report file. It is possible to use masses other than Mass M+0 default fraction trigger. Mass M+0 is no longer the default fraction trigger. Now the fraction trigger must be specified as the mass in the sample list plus the adduct in the FractionLynx method. AutoMIT assigns a specific minimum intensity threshold (MIT) value for each sample derived from the background response of a blank injection. The Waters ELSD detector may be used to trigger fractions As a user option, all stages of AutoPurify run sequentially when submitted through OALogin, with no interruptions by samples owned by other users. Allow selection of Minimum Intensity Threshold (MIT) file per narrow and generic method. Allow selection of MIT file on Walkup page for use with Open Access FractionLynx. Report Collected Volumes in FractionLynx report files (FPT) file. An option to select best tube using intensity of targets. Select pool indices using intensity of targets. An option to group fractions separated by a small time in tube selection and pooling. Check the RT and % total area for a specified set of chromatograms. Allow user to monitor at least 5 peaks in QC. MassLynx 4.1 Release Notes 716001833 / A 3-11

Allow separate processing parameters for MS positive ion and MS negative ion data. Perform QC Intensity test on multiple masses. Improved mixed trigger support in AutoPurify preparative stage OLB generation Emergency Collection starts correctly when triggered before the first fraction (TI 20101, TGR 1992). Sample Purity not generated for Mass Target and UV Wav trace (TI 17183, TGR 463).. Waste is treated as a peak when fraction trigger times are used for combine times (TI 18832 TGR 643). FractionLynx browser Help Library LogLynx As a user option, each sample can be printed as a separate job. FractionLynx report files (*.fpt) can be exported in *.txt, *.tab, *.csv and XML formats. QC information can be displayed in the FractionLynx Browser. FractionLynx Browser reports well location as a sequential location with X,Y referencing enabled (TI 17776, TGR 2190). An HTML online help system is available for MassLynx, Inlet Control, MS Instruments and Application Managers. The Forward (For) or Reverse (Rev) field name is appropriately capitalized based on selection (TI 17986, TGR 506). The Entry field in the Hit List window of Library is initially available (TI 17988, TGR 507). LogLynx Audit Trail opens at beginning of log (TI 16390, TGR 177). MALDI PSD Two application managers are added: one that facilitates calibration by transforming PSD MX, and one that matches fragment ions to a precursor. 3-12 716001833 / A MassLynx 4.1 Release Notes

Calibration Application manager that transforms PSD MX data to aid the calibration process. Simple method editor for setting parameters. A browser showing residual graphs and summary tables that update as calibration proceeds. Color-coded segment data Export the current calibration at any stage of the calibration procedure. Full printing and reporting capability. PSD MX MarkerLynx Application manager that matches fragment ions to precursor. Fragment spectra suitable for peptide database searching. Simple method for setting parameters. An option to apply a peptide filter before fragment matching. Multiple precursor ions processed simultaneously. Precursor ions can be imported via a raw or text file. Simple view of precursor ions and fragment spectra. Readily export fragment spectra as pkl files. Stitch fragment data within the browser application. Create a raw file containing the stitched fragment data and corresponding fragment spectrum. Full printing and reporting capability. Markers detected in dead time are highlighted in the Marker table An option to mean-center the data for PCA. A processing dialog has been added. Improved peak detection and quantitation. Updated export template for SIMCA. An option to select the mass-to-charge range. Detected chromatographic peaks are annotated in the chromatogram view. An option to de-isotope data. Automatic link to SIMCA-P+. MassLynx Top Level MassLynx 4.1 Release Notes 716001833 / A 3-13

MassLynx 4.1 provides an information-gathering utility. The utility operates with default settings and includes a user interface to configure additional files. You can browse the Information Gathering log. MassLynx 4.1 provides the Black Box error trapping tool of Identify Software. It is disabled by default. When enabled as directed by Waters Support Personnel, Black Box provides diagnostic information related to system errors. MassLynx recognizes radio-labeled formulas in Elemental Composition, Isotope Modeling, Molecular Weight Calculator, and MetaboLynx. Blank Injection Processing should allow retention time window per data type. Preemptive scheduling is disabled in Full Security. Drive A is not accessed when browsing in MassLynx 4.0 (TI Tracker 11717, TGR 273). Comma is supported as the decimal separator for Spectrum, Chromatogram, and QuanLynx data (TI 13952, TGR 178). Priority sample designation is configurable property by user (TI 11172, TGR 1829). Sample Logging Database no longer disabled after a MassLynx crash (TI 20499, TGR 2148). MetaboLynx setup and processing For pharmaceutical users, an assay feature for processing multiple analytes, comparing metabolites of the first with the remainder, as in an assay of multiple species, or a comparison of inhibited samples against a primary uninhibited analyte sample. Expected metabolite list includes optional retention time. Metabolite list can be set up from the browser commands "Copy Nominal/Accurate Metabolite List for Setup." Allows searching in the browser for an Internal Standard used for peak area ratios. The mass is named "Internal Standard." In the Browser, the "IS Area Ratio" column reports values equal to IS Peak Area / Metabolite Peak Area for all valid metabolites. In the case of multiple entries for the internal standard, the one with the largest peak area becomes the numerator. Expected metabolite list has an extended set of default bio transformations. Unexpected Metabolites are searched against all sample list precursor masses, not just Mass A, to find the best fit. Additional elemental composition options. Mass range chromatograms can be specified relative to the parent mass. Mass range chromatograms offer the option to discard traces that contain no peaks. 3-14 716001833 / A MassLynx 4.1 Release Notes

Peak detection method is set to ApexTrack by default. Enabled ISO option on Unexpected Metabolite tab. Metabolite list order set to Ascending Mass. Separate RPT files for Different Sample Groups in the Sample List. Procedure to combine accurate mass spectra is simplified. Invalid metabolites and overcomplicated metabolite names are not reported (TGR 531). MetaboLynx browser NeoLynx AutoStart MS/MS options. Browser chromatogram peak annotation options include formula and metabolite name/label. Modification of Multiple Entries in a metabolite table Data filters offer as options (1) Retention Time and (2) No Elemental Compositions. Metabolic stability analysis reports intrinsic clearance when ConcA is specified on the sample list. Default plate description to override a specified plate. The metabolic stability analysis allows metabolite-naming to be rounded to a specified accuracy (TI 18460). Browser command "File, Properties" reports file statistics generated during processing. Report orientation is saved between printouts. Print of analyte and control trace positioned overlaid instead of one above the other (TI 21139, TGR 1833). OpenLynx Samples with null result create blank cells so that the samples that follow are reported correctly in NeoLynx (TI 15119, TGR 167). Neutral-loss acquisitions are calibrated (TI 18433, TGR 525) Spare fields for the sample list are reportable in the OpenLynx report file. User may monitor at least five peaks in QC. The QC intensity test is available for multiple masses. MassLynx 4.1 Release Notes 716001833 / A 3-15