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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
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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


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accuracy, and organization of our documentation. You can reach us at
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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 Waters-
supplied 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 Fault fixes in MassLynx 4.1 ........................................................3-1


Mass Spectrometer Enhancements and Fault fixes ................................................. 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 Fault fixes........................................................................ 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:

Minimum firmware requirements


Product Minimum Version verification Upgrade part number
version
Revision displayed on the CPU
996 PDA detector 1.8 board. (1.8 EPROM) N/A

(no other versions


available)

2996 PDA detector 3.5 N/A

(no other versions


available)

W2487 UV detector 1.02 Revision displayed in the Performed at no charge


detector’s diagnostics by a Waters Service
and in the System Engineer
Information window.

W2488 MUX UV 2.01 Revision displayed in the Part number


detector detector’s diagnostics 361000213
and in the System
Information window.

Waters 2420 ELSD 1.0 Revision displayed in the N/A


detector detector’s diagnostics
and in the System
Information window.

busSAT/IN 20.0 Label on the PCB WAT200415


(busSAT/IN Module)

Alliance 2690/2695 2.03 Displayed at power-on 667000509EN


separations module

2796 bioAlliance 2.1 Displayed at power-on N/A


2790/2795
separations module

MassLynx 4.1 Release Notes 716001833 / A 1-3


Minimum firmware requirements
Product Minimum Version verification Upgrade part number
version

Alliance 2796 2.1 Displayed at power-on N/A


bioseparations module

515 pump 1.0 Displayed at power-on N/A

(no other versions


available)

Pump control module 2.2 N/A N/A

Pump control module 3.0 N/A N/A


II

1525 pump 1.3 N/A N/A

(no other version (no other version


available) available)

1525µ pump, 1525EF 2.01 or N/A N/A


pump 2.02
(no other version (no other versions
available) 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 1.08 Part number


pump 361000215

C/FO 1.05 N/A

(no other version


available)

2767 sample manager All N/A

(no other version


available)

1-4 716001833 / A MassLynx 4.1 Release Notes


Minimum firmware requirements
Product Minimum Version verification Upgrade part number
version

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 All

ACQUITY binary 1.20 Displayed in ACQUITY


solvent manager Console.

Select "View Module


Info"

ACQUITY sample 1.20 Displayed in ACQUITY


manager (autosampler Console.

Select "View Module


Info"

ACQUITY TUV 1,20 Displayed in ACQUITY


detector Console.

Select ‘View Module Info’

ACQUITY Sample 1,20 Displayed in ACQUITY


Organizer Console.

Select ‘View Module Info’

ACQUITY 2996 PDA 1.10


detector; ACQUITY
UPLC TUV Detector

ACQUITY UPLC 2996 4.10 Displayed in ACQUITY


detector Console.

Select ‘View Module Info’

MassLynx 4.1 Release Notes 716001833 / A 1-5


Minimum firmware requirements
Product Minimum Version verification Upgrade part number
version

ACQUITY ELSD 1.20 Displayed in ACQUITY


detector Console.

Select ‘View Module Info’

ACQUITY ELSD N/A Will be specified on


Detector 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 UV-
only 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 Supported Firmware


Standard Agilent 1100 systems (w/
G1323A Control module)
G1310A* A.05.01, A.04.11, A.04.06, A.03.81,
A.03.60, A.03.32, A.03.50
G1311A quaternary pump* A.05.01, A.04.11, A.04.06, A.03.81,
A.03.60, A.03.32, A.03.50
G1312A binary pump* A.05.01, A.04.11, A.04.06, A.03.81,
A.03.60, A.03.32, A.03.50
G1313A Auto-sampler A.05.04 A.05.01, A.04.10, A.04.06,
A.03.80, A.03.61, A.03.30, A.03.31
G1314A VWD A.05.01, A.04.10, A.04.06, A.03.80,
A.03.60, A.03.30
G1315A DAD detector * A.05.01, A.04.11, A.04.06, A.03.80,
A.03.61, A.03.30
G1315B DAD detector * A.04.11, A.04.06, A.03.80, A.03.61,
A.03.30
G1316A column heater A.05.01, A.04.11, A.04.06, A.03.80,
A.03.90, A.03.60, A.03.30
G1323A HPLC controller A.02.10, A.02.02
G1326A HPLC controller Firmware version not available
/verified
G1327A autosampler Firmware version not available
/verified
G1329A thermostatic 5.01, A.04.10, A.04.06, A.03.61,
autosampler A.03.80x, A.03.61, A.03.30, A.03.31
G1330A Thermostatic Auto- Firmware version not available
sampler) /verified
G1368A Agilent 1100 Well plate A.04.08
autosampler (includes.
thermostatic option)
G1367 microtitre plate A.05.04
autosampler
G1389A MicroALS autosampler A.04.06
includes thermostatic option
G1376A capillary HPLC pump A.05.04 A.04.08
G1379A de-gasser 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 Firmware
HP6890 A.05.04,05.05
HP6890N 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 233
Version1.02
322 Nebula 215 (FW Version 2.20)
QuadZ-215 (FW Version 1.7)

JASCO system

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 Firmware


Oven
LC- 5.27 SIL-10ADvp 5.32 CTO- 5.24
10ADvp 10ASvp
LC-10AD N/A SIL-10A N/A CTO- N/A
10Avp*
LC- N/A SIL-10Ai N/A CTO- N/A
10ATvp 10ACvp*
LC-10AT N/A SIL-10Axl N/A CTO- N/A
10A*
LC-10AS N/A SIL-HTc 6.03 CTO- N/A
10AC*
LC-10Ai N/A SIL-HTa 6.03
LC-8A N/A
LC-7A N/A
LC-6AD N/A

MassLynx 4.1 Release Notes 716001833 / A 1-9


Shimadzu system (continued)

System Firmware Fraction Firmware Detectors Firmware


Controller
Collector
SCL- 5.42 FRC-10A N/A APD-10Avp N/A
10Avp
SPD- 5.23
10AVvp
SPD- N/A
10Avp*
SPD-10A* N/A
SPD-10AV* N/A

N/A – Firmware version not available /verified

CTC Pal system

Autosampler Firmware
CTC Combi PAL (Cycle Composer N/A
V1.4 required)
CTC GCPAL N/A
CTC A200S/SE N/A
CTC HTS PAL 2.2.4 , 2.4.0
CTC HTS PAL– Harney Valve 4 way 2.2.4,2.4.0
injection supported

N/A – Firmware version not available /verified

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


Windows Updates For Windows 2000 SP4
MSXML 4.0
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 Fault fixes 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 Fault fixes.
Enhancements are described following the heading. Fault fixes are labeled.

Mass Spectrometer Enhancements and Fault fixes


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.
Fault fixes
• 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.
Fault fixes
• 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.
Fault fixes
• 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


Fault fixes
• 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
Fault fixes
• 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
Fault fixes
• 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
Fault fixes
• 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.
Fault fixes
• 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
Fault fixes
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)
Fault fixes
Redundant TDC edge control and gain settings are removed (TI 21702, TGR 2196).

Q-Tof Premier
• 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

Q-Tof API

3-4 716001833 / A MassLynx 4.1 Release Notes


Fault fixes
• 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).

Q-Tof Global
Fault fixes
• Instruments fitted with TTP 4GHz TDC cards maintain configuration setting (TI
20475, TGR 1666).

Q-Tof Micro
Fault fixes
• 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 Fault fixes
Overall new features and enhancements
• 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.

ACQUITY
• 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).
Fault fixes
• Agilent 1100 UV operates with 2700 sampler (TI 15899, TGR 155).
• Agilent/HP 1090
• Fault fixes
• TI 15298 TGR 146 WashOn feature is reinstated for the Agilent 1090
autosampler.

3-6 716001833 / A MassLynx 4.1 Release Notes


HP 6890
Fault fixes
• 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).

Jasco
MassLynx 4.1 supports control of JASCO devices with LC NET II box.
Fault fixes
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.
Fault fixes
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.
Fault fixes
• 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.
Fault fixes
• 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.
Fault fixes
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 )


• Supports automatic peak detection parameters for accurate mass.
• Supports continuous lock mass correction for continuum data.

AutoLynx
Printing from FractionLynx report files (FPT) files via AutoLynx.

AutoPurify
• 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.
Fault fixes
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
Fault fixes
• 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
• 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.
Fault fixes
FractionLynx Browser reports well location as a sequential location with X,Y
referencing enabled (TI 17776, TGR 2190).

Help
An HTML online help system is available for MassLynx, Inlet Control, MS
Instruments and Application Managers.

Library
Fault fixes
• 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
Fault fixes
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
• 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.

MarkerLynx
• 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.
Fault fixes
• 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.
Fault fixes
• Invalid metabolites and overcomplicated metabolite names are not reported
(TGR 531).

MetaboLynx browser
• 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.
Fault fixes
Print of analyte and control trace positioned overlaid instead of one above the other
(TI 21139, TGR 1833).

NeoLynx
Fault fixes
• 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)

OpenLynx
• 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


• MS positive and MS negative data can be processed applying different
processing parameters.
• Optimized elemental composition prediction (i-Fit Algorithm) is available in
OpenLynx processing.
• OpenLynx supports continuous lock mass correction via "All File Accurate
Mass Measure" (AFAMM).
Fault fixes
• OpenLynx MS upper and lower analyte limits (counts) applied correctly (TI
16236, TGR 518).
• Peaks which are numbered alike but which have different retention times are
no longer produced (TI 24498, TGR 3764).
• OpenLynx editor overwrites olp file on opening with previous olp file values (TI
24567, TGR 3711).

OpenLynx browser
• As a user option, each sample can be printed as a separate job.
• OpenLynx report files (*.rpt) can be exported in *.txt, *.tab, *.csv and XML
formats.
• OpenLynx supports printing and exporting of adduct-dependent fields.
• QC information can be displayed in the OpenLynx Browser.
Fault fixes
• Export displays data from wrong trace (TI 15131, TGR 53).
• Observed mass incorrect on production of text file (TI 13718, TGR 8).
• Printing side-by-side spectra causes gaps in the printout (TI 15771, TGR 176).
• OpenLynx Browser generates an error when printing ErrorPPM or ErrormDa
(TI 21636, TGR 2051).
• OpenLynx prints full UV chromatogram range (0 min-end of run) even though
the set range is different (TI 20951, TGR 2052).
• Peak integration window now does not show area below the integrated peak as
being part of the area included in the calculation.

OpenLynx Open Access Login


• Sample list order maintained with multiple plates.
• Mixed Triggers supported on Walk-up page.
• Separate QC methods are available for analytical and preparative separations.
• Preparative QC vial location can differ from that for an analytical vial.
• Administrator may define the methods available to individual users.
• Text field content optionally is validated using regular expression definitions.

3-16 716001833 / A MassLynx 4.1 Release Notes


• OALogin supports usernames and passwords. Use of passwords is an
administrator-controlled option. Passwords are stored in an encrypted format.
• If passwords are not enabled, any user may create users if the administrator
permits.
• Optional user entry of HPLC parameters (including gradient table) at sample
login for Waters 2795 and Agilent HP1100 series of instruments.
• Peak integration window no longer represents the area below the integrated
peak as part of the area included in the calculation.

OpenLynx Toolkit
OpenLynx Toolkit, described in the online (OpenLynx Toolkit) Help, is for OpenLynx
OALogin administrators.

Printing
Fault fixes
Experiment report pages are numbered correctly (TI 22379, TGR 3197).

ProfileLynx
• Time trend plots for functions.
• Sample retention time windows are derived from the calibration curve used for
peak selection.
• Ability to edit calibration-type chromatograms.
• Support for Multipoint quantification calibration.

Quan Optimize
• Installed as a separate application manager.
• Multiple QuanOptimize batches can be added to a MassLynx queue.
• Supports optimization in ESCI mode.
• Generates a compound method results library.
• Can create SIR method as well as MRM for QuanOptimize results.
• Supports optimization of multiple ions per compound.
• OAQuanOptimise permits column selection during login.
Fault fixes
Creation of unique curve files in QuanLynx processing limited to 999 files (TGR
527).

QuanLynx
• QuanLynx 4.1 Method Editor revised to new format.
• Bracketed standards are available

MassLynx 4.1 Release Notes 716001833 / A 3-17


• QuanLynx can print the experimental record.
• A user option, each sample can be printed as a separate job.
• A method interprets Mass A and Wavelength A from the sample list.
• Can exclude points from calibration curve from summary table list.
• Quantitates an unknown compound by assigning a known alternative
calibration.
• Can report baseline heights at peak start and peak end.
• Can report peak start and peak end times.
• Sample fields in the report formats are configurable.
• Incorporates multiple trace data with interference detection.
• Paper margins for report printing are definable.
Fault fixes
• Double-clicking on Summary table works (TI 17650, TGR 473).
• Reports a concentration when an area/response is present. (TI 17150, TGR
432).
• Header information (user name) printed in reports (TI 16699, TGR 343).
• When browsing in a calibration file, the browser locates correct file type (TI
14572, TGR 1581).
• Updated R.T. values are correct when dragging peaks into the method editor
(TI 22964, TGR 2872).

Waters NuGenesis Scientific Data Management System (SDMS)


• Access to SDMS is integrated into MassLynx 4.1.
• Links between MassLynx and SDMS are definable from MassLynx.
• MassLynx Data files can be archived in SDMS.

MassLynx Security
MassLynx 4.1 introduces significant enhancements to MassLynx compliance tools.
Full details are available in the MassLynx 4.1 Security Guide, part of the MassLynx
4.1 Documentation Set.

• MassLynx Full Security uses a folder-level checksum model rather than the
Secure Files Model used in version 4.0.
• It is possible to acquire data directly to network file shares in Full Security.
• Users may override the current user to access the system as a different user
(multi-user) while the system is acquiring data.
• BackLynx is not required to move files from Full Security installations.

3-18 716001833 / A MassLynx 4.1 Release Notes


• Unregulated user group permissions allow unregulated operation in defined
directories.
• Files (methods, etc) can be imported to regulated projects from unregulated
projects.
• Only regulated or unregulated log-ons are permitted at any one time.
• Methods as well as raw data and processed results can be signed in full
security.
• Access to directories is by user group.
• Predefined reasons for change can be defined that are specific to the action
undertaken.
• User groups can be allocated specific folders for data acquisition and
processing.
Fault fixes
• Secure files electronic signatures are not registered unless “force signatures” is
enabled (TI 18052, TGR 514).
• A tamper warning appears when you create a spectrum from a chromatogram
using combine function (TI 19173, TGR 683).

Shutdown
Fault fixes
• Shutdown triggers only when the error type is configured to cause the
shutdown. That is, an HPLC or MS error activates shutdown only when the
instruments involved are enabled for shutdown on error (TI 18516 TGR 612).
• Shutdown method operates with the ACQUITY system (TI 21616 TGR 2260).

Spectrum
• Spectrum operates with Accurate Mass.
• Lock mass is read from experiment file.
• Spectrum optionally displays “daughter” or “parent” ions.
• “Show transition label” is available in peak annotation settings.
• Errors should be displayed in the spectrum list.
Fault fixes
• It is possible to recalibrate a file from the spectrum window without the
relevant permission (TI 22967 TGR 2832).
• Mass measure operates with LockSpray (TI 21286, TGR 2147).

Strip
Fault fixes
Points with intensity of zero added during the enhance process (TI 15982 TGR 195).
MassLynx 4.1 Release Notes 716001833 / A 3-19
TargetLynx
• The Overview pane can be printed.
• TargetLynx can print the Experimental record.
• As a user option each sample may print as a separate job.
• TargetLynx Method to interpret Mass A and Wavelength A from sample list.
• Ability to exclude points from calibration curve from summary table list.
• Quantitate unknown compound by assigning known alternative calibration.
• Baseline heights at peak start and peak end are reportable.
• Peak start and peak end times are reportable.
• Sample fields in the report formats are configurable.
• Add display of multiple trace data, with interference detection, to TargetLynx.
• User may define paper margin dimensions for hardcopy report printing.
• The Overview pane may be printed.
• It is possible to specify secondary ion detection RT window around primary ion
RT.
• Peak quality measurements are reported in the overview window.
• Bracketed standards are available.
• You can define printed headers in TargetLynx reports.
• Improved TargetLynx printing templates for chromatograms.
• Ion ratios and retention times may be averaged over multiple samples.
Fault fixes
• Can drag confirmation traces into the chromatogram window (TI 19251, TGR
757).
• Can report r2 values greater than 0.999 (TI 19251, TGR 758).

3-20 716001833 / A MassLynx 4.1 Release Notes


4 MassLynx 4.1 Software Notes
Mass spectrometer control notes
All Mass Spectrometers
• When toggling from absolute to relative intensity on the Tune page, the
display mode does not switch (TGR 1416).
• If you open MassLynx when the mass spectrometer's embedded PC is not
connected, the Tune page might fail to appear. To ensure the Tune page's
appearance, set the registry key,
HKEY_LOCAL_MACHINE\\SOFTWARE\\Micromass\\MassLynx\\ShowSplas
hScreen, to zero.

All Quadrupole Mass Spectrometers


The calibration now reports RMS residual values instead of standard deviation.
The maximum RMS residual can be set in the Automatic Calibration Check
window. Residual plots are contained in the calibration report. Previous versions
of MassLynx also contained mass difference plots in the calibration report (TGR
2786).

All MS with ESCI


If an MS Method is created with functions staggered in time and with of differing
polarity, the MS method produces warnings indicating that it cannot reorder the
functions in the experiment. The experiment can still be saved. (TGR 3895)

AutoTune for quadrupole mass spectrometers (ZQ, Quattro micro, Quattro Premier,
Quattro Premier XE)
• When you use AutoTune, the syringe pump flow rate is fixed at 10 uL/min. If
the detector signal is too small or saturated, adjust the concentrations of
compounds in the tuning solution (TGR 2479, TGR 3344).
• If a user has the Create Tune File privilege but not the Alter Tune File
privilege AutoTune—Full is unavailable (TGR 3772).
• When running AutoTune with full security and acquiring data over a network,
you are prompted to save the tune file (TGR 3786).
• AutoTune is not available for dual ionization modes (ESCi, APCI/APPI) (TGR
2808).
• When developing MRM methods for multiple product ions, validate the quality
of the detected fragments (TGR 3729).

MassLynx 4.1 Release Notes 716001833 / A 4-1


AutoSpec
The Y-focus table is not applied when an acquisition is run from the Tune page. For
Tune page acquisitions, you must acquire from the sample list, or save the file as
Default.pro\acqudb\default.ypr.

LCT
• Network acquisitions are not supported.
• Acquisitions with Positive/Negative switching are not supported on the LCT
when equipped with TTP TDC cards (TGR 3249).
• Event out control is not operational.

LCT Premier
• Network acquisitions are not supported.
• DRE cannot detect isotopes of multiply charged ions when the detector is
saturated (TGR 1259).
• Begin tuning before changing LockSpray to the reference mode for non-
storage acquisition (TGR 76).
• Manually set the Tune page scope scale for centroid data (TGR 61).
• Ensure the LockSpray cable is connected before initializing the Tune page
(TGR 421).
• Some Rf settings and the DRE magnification factor are not stored in the
experimental record (TGR 3317).
• After completing a MassLynx repair installation, the LockSpray is not
available. To make it available, reselect it from Instrument/Options, on the
shortcut bar (TI 21646, TGR 2239).
• The tune page might close spontaneously if you click Cancel during a running
wizard. To resume communication, proceed as follows:
1. Close MassLynx and reboot the PC
2. Click Start > Run.
3. Type telnet EPC.
4. At the > prompt, type "reboot" and press Return.
5. When the instruments sound a three-tone chime, restart MassLynx and
the Tune page.
• The reflectron, flight tube and resolution values should not be modified once
the Setup and Calibration wizards successfully run. Internal checks on these
tune parameters permit some modification to their values without
invalidating the Accurate Mass indicator status, leading to an undesirable
mass shift (TGR 3948).

4-2 716001833 / A MassLynx 4.1 Release Notes


• Statistical accurate mass errors are not shown on the external lock mass lock
spray function when running a real time centroid experiment. Internal lock
mass corrected centroid data is unaffected (TGR 3953).
• When operating the LCT Premier with accurate mass wizards (workaround for
TGR 3774, 3939), follow this procedure exactly to ensure trouble-free setup of
Exact Mass and to see statistical errors regarding your acquired data.
1. Click Calibration > Calibrate Tof and Load default.cal. Then close the
dialog box.
Requirement: This dialog must remain closed when running any
of the wizards, unless the procedure specifies otherwise.
2. Using a reference compound (e.g. leucine enkephalin) infused via the
reference channel, tune the instrument for each of the four modes (V+,
V-, W+, W-) you intend to use. The resolution should be 8000-10000
for V-mode and 15000-18000 for W-mode. The sensitivity should also
be maximized using the cone voltage, capillary, and collision energy.
3. Switch the Tune page to the mode you want to set up first for exact
mass. Then launch the Accurate Mass Set Up wizard from the Toolbar
button or the Wizards > Accurate Mass option. The instrument must
be in Operate mode for one hour before you can access these buttons .
Be sure to select the reference compound from the list that matches the
current polarity mode of the instrument.
4. On successfully completing the wizard, accept the result. If the wizard
fails due to a weak beam, re-optimize the beam's intensity or prepare
fresh reference compound.
5. Repeat steps 3 and 4 for each of the modes you intend to use.
6. Switch to the analyte channel, and infuse an appropriate calibration
compound like sodium formate solution.
7. Click Calibration > Calibrate Tof and Load default.cal, Then close the
dialog box.
8. Launch the Calibration wizard from the Toolbar button, or use the
Wizards > Calibration option. You must specify the same calibration
filename each time you run the calibration wizard, regardless of mode.
When setting up the wizard,
• Ensure that you select the appropriate reference file (compound
and polarity).
• Define the mass range over which you intend to calibrate. Note
that you may need to reduce the selected mass range if your
calibrant shows a wide intensity range between different reference
ions.
9. On completing the wizard, review and amend the peak matches in the
Calibration Results browser, and accept the result. A small green
square appears in the Exact Mass Status indicator.

MassLynx 4.1 Release Notes 716001833 / A 4-3


10. Switch to the next mode you intend to calibrate, and repeat steps 8 and
9. Once the process is complete, green indicators in the accurate mass
toolbar indicate the instrument is exact-mass-ready for all the modes
you established. When you now run an acquisition in an exact-mass-
ready ion mode, you see statistical mass errors displayed in brackets
next to the mass in the Spectrum browser window. Note that if errors
are not displayed, one of these checks could have failed at the outset of
the run:
• The MS method data type is not centroid.
• No lock mass is defined in the MS method or lock mass m/z is
outside the calibrated range.
• The mass range defined in MS method is outside the calibrated
mass range.
• Pusher cycle time mismatch between the MS method and the
calibration
Find more information about pre-acquisition checks in the "Running
the Accurate Mass Wizards" section of the instrument's acquisition
guide. You can also access the information by clicking "?" (online Help)
on the Accurate Mass toolbar.

M@LDI
• Network acquisitions are not supported.
• M@LDI systems are not supported in MassLynx Full Security.
• Always calibrate the instrument before acquiring data from the sample list
(TGR 1318).
• In multifunction experiments, all functions d have the same mass ranges
(TGR 1321).
• Ensure the PAD has finished moving before changing high mass detect
settings (TGR 1769).
• Always use the Browse facility to select methods in the sample list (TGR
1773).

MALDI Micro MX
• Network acquisitions are not supported.
• MALDI Micro MX is not supported in MassLynx Full Security.

Q-Tof Ultima API, Q-Tof API-US


• Network acquisitions are not supported.
• Sample list queue may stall when Step Collision Energy is enabled (TI 21959,
TGR 2772).

4-4 716001833 / A MassLynx 4.1 Release Notes


• The gas control buttons occasionally are unresponsive, requiring two or more
clicks to activate them. (TGR 3709).
• Auto MCP Conditioning does not work (TGR 3753)

Q-Tof Micro
• Network acquisitions are not supported.
• For survey experiments the first scan of reference function is recorded as 0,
although all scans have signal (TGR 631).
• After the installation, open, close and reopen the Tune page to enable the
syringe pump (TGR 893).
• Should the peak display freeze when changing the ion mode or leaving the
quad set-up mode, reinitialize the Tune page to recover the peak display (TGR
894).
• MCA with LockSpray combines the sample and LockSpray functions into one
spectrum (TGR 900).
• The Collision energy value, in the spectrum, is offset by one scan when
running a profile acquisition. It is necessary to manually match the CE with
the scan. (TGR 902).
• Ensure LockSpray frequency is greater than the total time for all functions
(TGR 3138).
• You cannot run a method with more than one function whose data format is
MCA (TGR 3547).
• You cannot invoke Startup/Shutdown on gas fail (TGR 3554).
• You cannot run methods with more than one function of differing data format
with LockSpray (TGR 3563).
• You cannot operate with an inter scan delay of 0 (TGR 3574).
• Event out control is not operational.

Q-Tof Premier
• Network acquisitions are not supported.
• DRE cannot detect isotopes of multiply-charged ions when the detector is
saturated (TGR 1259).
• When acquiring data with HV Ramping enabled, stop acquisition from the
Tune page, not the sample list ( TGR 1293).
• After conditioning the MCP, set the MCP voltage manually (TI 22153, TGR
2468).
• Scan Speed Comp calibration fails on missed reference peaks regardless of
acceptance criteria (TGR 1776).
• DDA charge state recognition uses Tune page collision energy, not the charge
state look-up files. (TGR 3246).

MassLynx 4.1 Release Notes 716001833 / A 4-5


• Do not add more than 5 EDC functions to an MS method (TGR 3119).
• If the sample list is used to specify the set mass for MSMS, the pusher
frequency for the first mass is always set to a value that suits the largest mass
in the list (TGR 3788).
• All peaks are flagged with uncertainty values in DDA if the mass calibration
has been created for a pusher frequency that differs from the frequency used
for Survey and MSMS. (TGR 3632)
• It should not possible to run the instrument at more than 10 scans per
second with 80% duty cycle. Nevertheless, the software allows you to set up
an experiment to achieve this (TGR 3755).
• It is not possible to acquire beyond mass 37048 (TGR 3817).
• It is not possible to define multiple custom lock masses (TGR 3851).
• In quad view, you must reinitialize the Tune page's peak display to update
settings. (TGR 3881)
• In quad view, with regard to the Tune page's peak display, the inter scan
delay can be ignored when changed. (TGR 3881)
• After the first switch from MALDI to ES following a clean install, a warning
dialog box appears. You can cancel it without consequence (TGR 3823).
• When operating the Q-Tof Premier with accurate mass wizards (workaround
for TGR 3774, 3939), follow this procedure exactly to ensure trouble-free
setup of Exact Mass and to see statistical errors regarding your acquired data.
1. Click Calibration > Calibrate Tof and Load default.cal. Then close the
dialog box.
Requirement: This dialog must remain closed when running any
of the wizards, unless the procedure specifies otherwise.
2. Using a reference compound (e.g. leucine enkephalin) infused via the
reference channel, tune the instrument for each of the four modes (V+,
V-, W+, W-) you intend to use. The resolution should be 8000-10000
for V-mode and 15000-18000 for W-mode. The sensitivity should also
be maximized using the cone voltage, capillary, and collision energy.
3. Switch the Tune page to the mode you want to set up first for exact
mass. Then launch the Accurate Mass Set Up wizard from the Toolbar
button or the Wizards > Accurate Mass option. The instrument must
be in Operate mode for one hour before you can access these buttons .
Be sure to select the reference compound from the list that matches the
current polarity mode of the instrument.
4. On successfully completing the wizard, accept the result. If the wizard
fails due to a weak beam, re-optimize the beam's intensity or prepare
fresh reference compound.
5. Repeat steps 3 and 4 for each of the modes you intend to use.
6. Switch to the analyte channel, and infuse an appropriate calibration
compound like sodium formate solution.

4-6 716001833 / A MassLynx 4.1 Release Notes


7. Click Calibration > Calibrate Tof and Load default.cal, Then close the
dialog box.
8. Launch the Calibration wizard from the Toolbar button, or use the
Wizards > Calibration option. You must specify the same calibration
filename each time you run the calibration wizard, regardless of mode.
When setting up the wizard,
• Ensure that you select the appropriate reference file (compound
and polarity).
• Define the mass range over which you intend to calibrate. Note
that you may need to reduce the selected mass range if your
calibrant shows a wide intensity range between different reference
ions.
9. On completing the wizard, review and amend the peak matches in the
Calibration Results browser, and accept the result. A small green
square appears in the Exact Mass Status indicator.
10. Switch to the next mode you intend to calibrate, and repeat steps 8 and
9. Once the process is complete, green indicators in the accurate mass
toolbar indicate the instrument is exact-mass-ready for all the modes
you established. When you now run an acquisition in an exact-mass-
ready ion mode, you see statistical mass errors displayed in brackets
next to the mass in the Spectrum browser window. Note that if errors
are not displayed, one of these checks could have failed at the outset of
the run:
• The MS method data type is not centroid.
• No lock mass is defined in the MS method or lock mass m/z is
outside the calibrated range.
• The mass range defined in MS method is outside the calibrated
mass range.
• Pusher cycle time mismatch between the MS method and the
calibration
Find more information about pre-acquisition checks in the "Running
the Accurate Mass Wizards" section of the instrument's acquisition
guide. You can also access the information by clicking "?" (online Help)
on the Accurate Mass toolbar.
• If, after setting up the instrument for exact mass, you must rerun the setup
wizard for any reason, you must rerun the calibration wizard for each mode
(TGR3939).
• When reviewing calibration results, do not clear the Calibration Parameter
Automatically Restrain Polynomial Coefficients box and accept the result.
Doing so results in incorrect behavior when statistical errors are calculated
on subsequently acquired data (TGR3947).
Note these recommendations when rerunning the calibration wizard (Q-Tof
Premier, LCT Premier)

MassLynx 4.1 Release Notes 716001833 / A 4-7


• Specify the same calibration file name is in the wizard for all ion
modes.
• When recalibrating the instrument for a different calibrant or over
a different mass range, specify the same file name in the wizard as
in the existing calibration.
• If you must use a different calibration file name, be aware that you
will need to rerun the calibration wizard in all of the other modes
to resume their exact-mass-ready state for the new calibration file.
Alternatively load the original calibration file. Note that the lock
mass wizard can be run independently, without rerunning the
setup wizard, using the Wizard > mass menu option (TGR3774).
• The tune page might spontaneously close if you click Cancel during a running
wizard. To resume communication, proceed as follows:
1. Close MassLynx and reboot the PC.
2. Click Start > Run.
3. Type telnet EPC.
4. At the > prompt, type "reboot," and press Return.
5. When the instruments sound a three-tone chime, restart
MassLynx and the Tune page.
• Rarely, after the Tune page spontaneously closes and you reboot according to
the preceding procedure, the API gas button fails to respond after restarting
MassLynx. Resume correct operation as follows:
1. Close MassLynx and reboot the PC.
2. On the rear panel of the instrument set the pump Override
switch to On.
3. Important: If you do set the pump Override switch to On, your
instrument vents at the next stage.
4. Switch the electronics circuit breaker, at the bottom of the
instrument's rear panel, to the down (Off) position.
5. Wait 5 seconds.
6. Switch the electronics circuit breaker to the up (On) position.
The electronics reset and the embedded PC reboots.
7. Wait for a three tone chime from the instrument, indicating that
rebooting was successful.
8. Run MassLynx, and open the Tune page. A message, “Warning
Pump Override Active,” appears at the bottom of the screen. On
the rear of the instrument, set the pump override switch to Auto
and the message disappears (TGR3937).

4-8 716001833 / A MassLynx 4.1 Release Notes


• The Flight Tube voltage (Engineer page) should always remain at the default
value (10.15kV) after the Setup and Calibration wizards successfully run.
Minor changes to this voltage (as little as +/- 0.01kV in W-mode) fail to
invalidate Accurate Mass checks and result in undesirable mass shifts of 0.2
Da. V-modes are unaffected (TGR 3948).

Quattro micro
APPI ion modes appear in the ion mode list, on the Survey Scan setup page, even
when APPI is not installed.

Quattro Micro GC
• On the probe ramp interface ensure Use Ramps is selected (TGR 1748).
• If AutoTune fails, manually reload the original tune file (TGR 1754).
• With either CI emission current or EI trap set to 0, switching from the standby
to operate mode may set filament current to 5A. Be prepared to reset the
current to a lower value (TI 23357, TGR 3092).

Quattro Premier
Negative values for analog channel are interpreted as "full scale" (TGR 3425).

Quattro Ultima
When running a positive/negative switching experiment, use values specified in an
MS method. Do not select Use Tune page (TGR 2754).

ZQ
Occasionally, the peak display can lose its calibration. However, data acquired to
disk are not affected. Closing the Tune page and deleting the file
nonstorageexp.exp remedies the problem. (TGR 3865)

MassLynx 4.1 Release Notes 716001833 / A 4-9


Inlet control notes
General information
• When logged on to the OS as a user without administrator privilege, the
Additional Status tab of the Inlet method editor will not be updated. Users can
overcome this issue by granting "Write" permission on the C:\Program
files\Waters Instrument folder for non administrative users.
• To avoid shutting down before the completion of run, ensure the end-of-batch
delay is greater than the run time for any HPLC or MS method (TGR 1377).
• For all WICS/ICOP and the Waters 2777/CTC PAL, any new projects need to
be cloned from Default.pro or a project originally derived from Default.pro.
• The Ethernet-controlled Waters 1525 Binary HPLC Pump cannot be
configured as part of a system that includes the Waters 2796 2D
Bioseparations Module.
• The Waters 1525 pump is controlled by installing Waters Pump Control
software. In any system using the 1525 the Gradient table should not contain
entries that are later than the inlet run time. The 1525 will continue to run
the gradient table until the gradient table time has finished.
• For all inlet systems with multiple pumps controlled by GPIB interface, the
pumps should be configured in ascending order (4,5,6,7, etc.). This applies
to MUX and staggered injection systems also.

ACQUITY
• Rebooting the MassLynx PC is required after installing ACQUITY software
(TGR 3242).
• PDA 2-dimensional channels, ELSD data, and diagnostic channels from
ACQUITY modules (e.g., pump pressure, various temperatures, etc.) are best
viewed in the Chromatogram window.
• When planning to quantitate ELSD and PDA 2-dimensional data with
QuanLynx, disable all ACQUITY diagnostic channels.
• When Acquiring across the network with an ACQUITY PDA, TUV, or ELS
detector, a maximum data rate of 20Hz is supported. Diagnostic channels
should not be enabled for network acquisitions. If you attempt to run greater
than 20 Hz with network acquisition enabled, a significant increase in inject
cycle time results.
• The real time update display will lag as much as 25% of the MBF
chromatogram run time. Additionally, the run time for the mass spectrometer
must be at least 0.1 minute longer than the detector run time to allow the
filtered data to be written to the file. (TGR 3791)

Gilson

4-10 716001833 / A MassLynx 4.1 Release Notes


Whenever a Rinse Injection Port step/function is added to the inlet method after a
gradient start, the injection port is washed before the gradient is started (TI 22139,
TGR 2968).

HP 1100
Sample list vial numbers have precedence over vial numbers embedded in the inlet
method (TGR 2516).

HP 6890
• Invalid injection volumes will not generate errors. However, no injection takes
place (TGR 1762).
• No warning is issued when the thermal injector is switched off and a method
downloaded. (TGR 3362).

Shimadzu (autosampler)
There is no access to the rinse mode, purge line, and rinse dip times in the method
editor (TI 20682 TGR 1840).

Waters 1525
Inlet editor displays pressure in psi and MassLynx main status page displays
pressure in bar. (TGR 3871)

Waters 2777/CTC HTS PAL


• All pre-SCN 509 or MassLynx 4.1 method files for Waters 2777/CTC HTS PAL
with the extension *.pma must be recreated in version 4.1 as *.cyx macros. A
license key is required to enable the Macro editor.
• When you operate using MassLynx Full Security, you must manually install
the Waters 2777/CTC HTS PAL. Restart MassLynx after the installation (TGR
403).
• After configuring the Waters 2777 you must establish communications with
the 2777, and then close and reopen the inlet method before all the fields are
available. It is not necessary to reset communications. (TGR 529).
• Local PC administrator rights are needed to install the Waters 2777 (TGR
1443).
• You cannot pause and restart a sample queue when an "inject ahead" method
is being performed. The queue must be stopped (TGR 3549).

Waters 2795 Separations Module


If Degasser control on 2795 Inlet dialog box is inactive, close and reopen the inlet
editor to activate it (TGR 2314).

Waters 2420 Evaporative Light Scattering Detector (ELSD)

MassLynx 4.1 Release Notes 716001833 / A 4-11


• MassLynx 4.1 supports only one Waters 2420 Evaporative Light Scattering
Detector. The 2420 is not supported with MUX MS, nor with the 2488 multi-
channel detector (TGR 212, 214).
• If the access permissions on the \Waters folder do not allow write access for
the currently logged-on OS user, invalid data might be written to the raw file
(TGR 3306).

Waters 600
• When configuring Waters 600 pumps with Waters Pump Control it is
recommended to use addresses for the pumps between 2 and 9. Do not use
addresses above 9

Waters SAT/IN
When acquiring data over a network or with Full Security, limit SAT/IN data rates
to 50 Hz. TGR 3307.

4-12 716001833 / A MassLynx 4.1 Release Notes


MassLynx software and application manager notes
Accurate Mass
• If you combine centroid data from the Chromatogram window by right clicking
and dragging across a range of scans with the mouse, the Automatic Combine
option will be used (and statistical errors displayed) only if the Process >
Combine Spectra… > Use Automatic Combine Parameters option is enabled.
You must access this menu to re-enable the option if statistical errors do not
appear on your combined spectrum TGR3949.
• The error displayed on an internal lock mass for centroid data is the
statistical error on the lock-mass peak combined with the error at that mass
from the original calibration. The error displayed on an analyte peak is the
statistical error on the analyte peak combined with the error at that mass
from the lock-mass modified calibration.
• Processing of a continuum data file with an internal lock mass (that is, no
reference LockSpray function) using APD, and specifying a lock mass, is thus
limited: The centroid data file resulting from this processing will show only
Exact Mass statistical errors for single scans. Combined scans will not show
the statistical errors. This limitation does not affect Continuum LockSpray
AFAMM processed data which shows statistical errors regardless of how many
scans are combined TGR3931.
• Errors displayed on combined AFAMM data may be unreliable where a peak is
flagged “!” in one or more of the individual scans. Errors displayed on
combined AFAMM data with an internal lock-mass do not take into account
the improvement in the lock-mass statistical error as more scans are
combined.

ChromaLynx
When converting MassLynx to NIST libraries if NIST 02 is not installed then a
directory C:\Nist02\MSSearch will need to be created manually or an error will occur

DataBridge
DataBridge conversions of files in the ASCII format to files in the MassLynx format
are limited to creating a single MassLynx Spectrum and not intended to produce a
full MassLynx RAW file. (TI 19401, TGR 628).

FractionLynx
• For FractionLynx, use a minimum mass spectrometer dwell time and inter scan
delay of 0.25 sec. For other data types, use a maximum of 2 pts/sec. (TGR 130).
• Some FractionLynx simulation description can be overwritten in the
chromatogram window if multiple simulations are performed on the same data
(TGR 3337).

MassLynx 4.1 Release Notes 716001833 / A 4-13


• When using FractionLynx with a multiple pump system ( FractionLynx with
Fraction Factory), you must insure that the MS run time is set at 20 seconds
longer than the UV detector run time. Additionally, the MAX data rate for the
2488 must be 2 Hz. FractionLynx errors will occur if this is not observed.

Installation
With Basic Security installed, it is necessary to reboot the MassLynx PC before
modifying the installation to add an additional application manager (TGR 1372)

MetaboLynx
Hovering windows over the MetaboLynx browser may prevent the correct redrawing of
molecules and metabolite tables.

NeoLynx
Spectra normalized to a peak in the browser are reset to 100% (TI 20401, TGR 1645).

Quan Optimize
Users must locate plates according to system indicates in QuanOptimise with
OALogin (TGR 1424)

QuanLynx
• Peak area threshold settings are global and not specifiable by data mode ( +/-)
(TGR 2258).
• Printed QuanLynx reports are available in black and white only (TI 19446, TGR
635).
• Ensure the method file is located in the project containing the data being
processed (TGR 1369).
• Where concentration values are reported to six or more decimal places, a variance
can arise between the initially reported values and those displayed after saving
and reopening QuanLynx, the result of rounding (TI 20822, TGR 1653).
• Integration parameters determined in Chromatogram must be manually entered in
the QuanLynx Editor (TI 21011, TGR 1949).
• Ensure the QuanLynx method editors are closed when calculating S/N in the
Chromatogram window (TGR 1580).

MassLynx Full Security


• For network file locations, disable virus-checking from the MassLynx PC (TGR
3284).
• When logging out of MassLynx, you must manually close any applications not
permitted for the next user. Ensure that local operating procedures define this
requirement (TGR 2218).

Spectrum

4-14 716001833 / A MassLynx 4.1 Release Notes


Extracting chromatograms from spectra at masses greater than 32000 Daltons may
result in zero intensity chromatograms (TGR 2440)

Startup and Shutdown


When the LC run time is longer than the MS run time, End of Batch shutdown
occurs, even when the LC is still running . To prevent such a shutdown, make sure
that the LC run time equals that of the MS. Alternatively, you can include a Stop LC
method task in the Shutdown task list or specify a shutdown delay (TGR 1377).

TargetLynx
• Peak Area Threshold settings are global, not settable by data mode( +/-) (TGR
2258).
• Printed TargetLynx reports are available in black and white only (TI 19446, TGR
635).
• Ensure the method file is located in the project containing the data being
processed (TGR 1369).
• Where concentration values are reported to six or more decimal places, the
initially reported values and those displayed after saving and reopening QuanLynx
can vary, the result of rounding (TI 20822, TGR 1653).
• Integration parameters determined in Chromatogram must be manually entered in
the TargetLynx Editor (TI 21011, TGR 1949).
• Ensure the TargetLynx method editors are closed when calculating S/N in the
Chromatogram window (TGR 1580).

MassLynx 4.1 Release Notes 716001833 / A 4-15

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