Waters MASSLYNX SOFTWARE

Flexibility, Confidence, Efficiency

ALL IN ONE PLATFORM 

[ MASSLYNX SOFTWARE ]

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SAMPLE ANALYSIS IS ALL ABOUT QUESTIONS 
Waters® MassLynx® Software is mass spectrometry 
software that answers those questions, helping 
your entire laboratory further advance. Productivity 
increases and training costs are lowered with our 
easy-to-use software. Run more samples faster with 
intelligent instrument control. Enhance confidence  
in your results with dedicated Application Managers 
that quantitate, identify, and confirm. Maintain 
compliance with integrated security features.

Mass Spectrometry 

labs are driven  

by results

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TAKE CONTROL OF MASS SPECTROMETRY ANALYSES
With today’s flexible instrument configurations, sophisticated data acquisition 
capabilities, and detailed data processing requirements for mass spectrometry  
(MS) analysis, it is easy to be overwhelmed when adding or replacing legacy  
MS instrumentation.

In the laboratory, the challenges of MS and MS/MS analyses are often compounded 
by the use of several types of analytical instruments and high personnel turnover.

To maintain – and even increase – laboratory productivity, you can turn to Waters 
software to simplify interaction with your MS system and retain the ability to perform 
advanced experiments.

MassLynx improves your MS system with its intuitive interface, intelligent instrument 
control, and software features built around the focus of your analysis: the sample. 
With much of its development driven by input from our extensive user base,  
MassLynx has evolved into a powerful software package that reflects the  
versatility and flexibility you require.

Balancing simplicity and sophistication, MassLynx makes MS and MS/MS  
techniques available to users of any skill level, from technicians to experienced  
mass spectrometrists.

INSTRUMENT CONTROL  
WITH THE SAMPLE LIST

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Launch inlet and MS  
method editors.

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Run step-by-step wizards to 
configure and optimize your 
instrument system.

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Specify instrument methods  
for individual samples or sets  
of samples.

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Start, stop, and monitor the  
progress of your experiments.

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View the status of system 
components, such as the inlet  
and mass spectrometer.

MassLynx offers versatile  

control of a range of Waters  

Mass Spectrometers, 

fully integrated with a suite  

of ACQUITY® UPLC®  

and ACQUITY UPC²® 

separations platforms.

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DATA MANAGEMENT  
WITH THE SAMPLE LIST

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Enter or import sample  
information in a versatile 
spreadsheet-style format.

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Directly access spectra  
and chromatograms.

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Initiate automated data  
processing and review with 
OpenLynx or TargetLynx XS.

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Access advanced application-
specific tools.

SAMPLE CENTRIC SIMPLICITY

Everything about your sample in one place
The challenge facing many laboratory analysts is not the speed of data acquisition, 
but the rate at which samples are converted into useful information.

MassLynx starts by giving you complete control of your analytical system within one 
interface: you will acquire, process data, and review results more productively than 
ever before. By using the individually designed and optimized data processing tools 
of MassLynx Application Managers, such as OpenLynx™ for processing batches of 
qualitative analyses and TargetLynx™ XS for quantification, samples are seamlessly 
converted into meaningful information – without manual data review. 

At the core of MassLynx is the Sample List: the single location for initiating all activities 
related to your sample. By presenting all the relevant sample information in one window, 
MassLynx’s Sample Centric™ approach simplifies your interaction with your MS system 
and increases the speed at which you convert samples into valuable knowledge.

The sample centric approach of MassLynx’s Sample 

List allows users to easily access instrument 

control, queue information, and system status, 

while viewing detailed sample information. In this 

example, parameters in the Sample List are set for 

a quantitative analysis using the TargetLynx XS 

Application Manager with ACQUITY UPLC I-Class 

and Xevo® TQ-S micro.

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USABILITY

Work intuitively with mass spectrometry
The user interface in MassLynx ensures direct, intuitive access to the functionality  
that you use most. The result is a user-friendly and fully comprehensive solution  
that will increase laboratory productivity.

The MassLynx toolbar, displayed alongside the Sample List, provides access at the 
click of a mouse to instrument status, sample queue information and Application 
Managers. You can easily switch from viewing the queue to viewing instrument  
status, or use the tabs to move between general and application-specific tools.

The ability to access basic sample information and system functionality through  
the MassLynx toolbar allows a novice user to successfully operate the system 
with a minimal learning curve.

This straightforward interface also gives the experienced user fast access to the 
advanced features MassLynx offers for sophisticated experiments.

VERSATILITY

Complete system solutions for sophisticated MS analysis
Waters combines the benefits of chromatographic separation and mass spectrometry 
as a powerful analytical technique, seamlessly controlled by a single software platform.

Together our instruments, software, chemistries, and comprehensive service and 
support bring you an integrated system that yields high sensitivity, robustness,  
and versatility.

GET THE MOST FROM 
YOUR HARDWARE, WITH 
SEAMLESS SOLUTIONS 
FOR ADVANCED 
APPLICATIONS

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Collect nominal or accurate 
mass MS and MS/MS data.

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Streamline data acquisition  
and processing.

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Acquire both low- and  
elevated-energy mass  
spectra with MS.E

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Real-time Data Directed Analysis 
(DDA™) allows you to 
automatically switch from  
MS to MS/MS acquisition  
when a compound of  
interest is detected.

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On-the-fly, automated accurate 
mass measurement using the 
internal reference standards 
from the LockSpray™ Source  
for Tof-MS systems.

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i-FIT™ algorithm for the 
Elemental Composition 
Calculator enables you to 
shorten predicted formulae lists 
for structural prediction in exact 
mass measurements.

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Control ionization sources 
including ESI, APCI, Multi-Mode 
Ionization, UniSpray,™ APPI/
APCI Dual Ionization, DESI, 
ASAP, APGC, and MALDI.

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Supports Waters and third-party 
inlets, autosamplers,  
and detectors.

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Improved system interaction
The real power of MassLynx lies in its 
ability to intelligently control an entire 
Waters MS system – from the sample 
and solvent management components 
to the mass spectrometer and auxiliary 
detectors. With an embedded PC 
acquisition system (EPCAS™),  
MassLynx puts intelligence and  
real-time functionality inside every  
mass spectrometer. 

MassLynx features IntelliStart™ for 
Waters MS Systems. IntelliStart 
integrates internal calibration fluidics 
and advanced diagnostics software,  
allowing the system to automatically 
tune, calibrate, and conduct full  
UPLC-MS/MS performance checks.

MassLynx provides intuitive data 
processing workflows for high-
performance analytical instruments. 
This eliminates the complexity that can 
be associated with high-resolution MS 
and ion mobility data.

MassLynx IntelliStart user interface integrates fluidics management with diagnostics software, allowing 

the system to automatically tune, calibrate, and conduct full UPLC-MS/MS performance checks. All you 

need to do is run your sample.

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MassLynx Security Manager 
Allows you to configure access privileges for each user, 
enabling you to easily deploy operator, administrator, and 
maintenance policies to meet your existing security 
protocols. Multiple user groups with access to alternative 
project areas are permitted fully-secured operation when 
required, and operation in less restrictive projects with  
less restrictive privileges when appropriate.

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Secure file encryption 
Employs the latest encryption and checksum technologies 
to prevent accidental or deliberate tampering with files.  
An optional component of the secure file system is the 
addition of electronic signatures.

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Audit log 
Provides an un-editable, hidden, encrypted file that 
automatically records all log-on and log-off events, security 
policy changes, MassLynx program module activity, and all 
events which relate to file generation or manipulation.  
This log file can be viewed and searched using LogLynx.™  
In addition to the audit log provided by the MassLynx 
security system, the TargetLynx XS Application Manager 
has a detailed audit log that records the specifics of 
quantitative data processing.

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Secure archival and retrieval 
Provides the ability to archive and then restore secure  
data without compromising date and file integrity.

  MassLynx integrates a complete Waters system, 

such as benchtop Xevo G2-XS QTof and  
ACQUITY UPLC I-Class for accurate mass 
measurement. Through MassLynx, you have 
complete control of the system itself, as well as 
the data processing tools you need to efficiently 
convert data into meaningful information.

COMPLIANCE

MAINTAINING SECURITY IN A REGULATED ENVIRONMENT
Strictly regulated laboratory environments place significant demands on LC-MS, LC-MS/MS, and GC-MS systems to maximize 
performance while also maintaining the security of data.

The MassLynx security system provides compliance-ready tools to meet GxP and 21 CFR Part 11 regulations. It is built on the latest 
file encryption, audit log, and secure archival/retrieval technology, and has been optimized for convenience and ease-of-use. The 
flexibility of the security system allows you to tailor and deploy security policies that meet the requirements of your laboratory.

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ADVANCED DATA MANAGEMENT

OpenLynx and TargetLynx XS Application Managers
OpenLynx and TargetLynx XS Application Managers are included with MassLynx. The OpenLynx Application Manager allows for 
customizable batch processing of qualitative MS information. OpenLynx includes quality control capabilities to ensure satisfactory 
system operation. The OpenLynx browser window facilitates review of large quantities of data; with its convenient plate viewer you 
can see at a glance whether individual wells contain the target analyte.

The TargetLynx XS Application Manager enables you to perform batch quantification, relying on our ApexTrack™ peak detection 
algorithm for optimized peak detection and integration. The TargetLynx XS browser contains all information required to review 
integration, calibration, and quantitation results. You may manually modify integration, enable and disable calibration points as 
needed, and recalculate the results following review. The internal audit log with configurable reasons for change and electronic 
signatures supports compliance with applicable regulations.

The comprehensive compliance tools allow for file generation, processing, reporting, archival, retrieval, and audit trails, with the 
ability to handle electronic signatures.

Data portability

OpenLynx and TargetLynx XS reports are self-

contained and may be automatically emailed 

when created using OpenLynx Open Access 

Software. The convenient browser software 

enables reports to be reviewed on any PC. 

TargetLynx XS reports permit interactive 

review, reintegration, and recalculation of 

results without MassLynx and access to the 

original raw data files. Multiple export formats, 

including *.txt, *.csv, *.xml, and HL7 compatible 

protocols, enable convenient data transfer to 

other software applications.

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FOR TARGETED ANALYSES

TargetLynx XS
Quantifying and confirming, TargetLynx XS delivers the information necessary for 
regulatory compliance. With a full range of automatic quality control checks for 
flagging out-of-range data, TargetLynx lets you identify at a glance samples that fall 
outside user-specified or regulatory thresholds.

QuanOptimize
Automating MS and MS/MS method development, QuanOptimize™ delivers high 
performance, high throughput quantification. Automated instrument optimization 
doesn’t stop at cone voltage, collision energy and MRM transition selection – 
QuanOptimize also identifies the best ionization method for each compound (ESI  
or APCI, positive or negative) and automatically quantitates and reports your batch.

OpenLynx Open Access Login
For walk-up analysis, OpenLynx Open Access Login offers multi-user and 
unsupervised sample login, backed by centralized system management.  
For LC-UV, LC-MS, LC-MS/MS, and GC-MS sample runs, from data acquisition  
to batch processing for qualitative and quantitative analysis, use OpenLynx to  
fully automate all stages in LC-MS quantification.

FractionLynx
Automating compound isolation and purification, FractionLynx™ controls fraction 
collection while tracking sample, fractions, and associated data. All possible through 
integrating versatile control of purification systems with an extensive and flexible set 
of compound detection, fraction triggering, and collection capabilities.

FOCUS THE POWER OF MS  
ON YOUR APPLICATION
The rate-determining step in many 
analyses is not data acquisition, 
but the speed your data can be 
converted into useful information.

To assist with both application 
specific data acquisition and the 
transformation of data into usable 
results, MassLynx offers Application 
Managers with specialized data 
processing functionalities that 
allow you to eliminate complex, time 
consuming manual data review.

FOCUS THE POWER OF MS  
ON YOUR LABORATORY  
TASKS AND INCREASE  
YOUR PRODUCTIVITY
The functionality of MassLynx 
Application Managers was guided 
by recommendations from our 
customers. We worked closely  
with labs like yours to better 
understand unique MS data 
processing challenges.

We developed these software 
extensions to improve your ability  
to control, collect, and process  
MS data for specific laboratory 
needs. The OpenLynx and 
TargetLynx XS Application 
Managers are included with  
each MassLynx installation.

Example of TargetLynx XS browser showing processed data.

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FOR IDENTIFICATION

ChromaLynx XS
Simplifying complex mixture analysis, ChromaLynx™ XS excels 
at semi-quantitative detection, identification and determination 
of components. Detecting and locating the maximum number 
of real components in a mixture, ChromaLynx also provides 
comparisons between a real sample and a blank to help 
determine common and unique components.

MetaboLynx XS
Automating metabolite identification, MetaboLynx™ XS 
leverages advanced comparison with control samples. You’ll 
miss fewer metabolites and accelerate your data interpretation. 
Advanced mass defect filters (MDF) let you concentrate 
on unexpected metabolites while the structural elucidation 
capabilities of MassFragment™ delivers the information you 
need to resolve metabolic pathways.

MassFragment
Automatically assigning collisionally activated dissociation 
mass spectra, MassFragment employs a novel systematic bond 
dissociation approach, rather than the traditional rule-based 
and rule-limited approach, delivering confident structural 
elucidation of your compounds.

MetaboLynx XS automates data processing for rapid metabolite identification. The unique structural elucidation capabilities of MassFragment for MetaboLynx 

interpret the enhanced fragment information from the SYNAPT® HDMS® for the most advanced characterization capabilities in small molecule profiling.

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WATERS GLOBAL SERVICES

Delivering world renowned 
services and support
Waters Service and Support 
offerings are tailored to optimize 
your laboratory productivity while 
addressing your budget realities. 
Our offerings help maintain system 
peak performance, minimize down 
time, address scientific application 
challenges, and support stringent 
compliance requirements. As your 
services and support provider, we 
are committed to the success of 
your laboratory and business.

Waters quality support and 
consultative services ensure  
your success wherever your 
laboratory is located in the world.

Waters has consecutively 
earned the ACE Award since 
2001 for providing best-in-class 
technical knowledge, issue 
resolution, and process support.

FOR BIOPHARMACEUTICAL IDENTIFICATION AND CHARACTERIZATION

BiopharmaLynx
Developed for confident characterization and optimized workflow, BiopharmaLynx™ 
leverages Waters’ leading protein informatics expertise. Determine the identity,  
purity, and stability of biopharmaceuticals, working with either peptide maps or  
intact proteins.

INTEGRATION WITH INFORMATICS SOLUTIONS
MassLynx is part of the Waters Laboratory Informatics suite, which offers complete 
solutions to improve your laboratory’s ability to capture data, secure information, and 
share knowledge. MassLynx offers tight, automated integration with our laboratory 
informatics solutions:

Progenesis QI
Progenesis® QI and Progenesis QI for proteomics enable you to accurately quantify 
and then identify the compounds and proteins in your omics samples that are 
significantly changing. Our unique approach to co-detection of compound ions is 
vital for accurate and precise quantification and access to a wide variety of search 
methods such as LipidBlast, ChemSpider and Elemental Composition gives great 
flexibility. Powerful data visualization’s and a guided-workflow give ease of use and 
great confidence in experimental results.

LiveID
LiveID™ Software enables the real-time classification of samples using direct analysis 
MS data. Compounds are measured in an unbiased fashion providing a holistic view 
of the sample. Initially, authentic verified samples are used to create and validate 
a multivariate statistical model. Validated models are then used to test samples to 
generate live classifications. The output is a simple yes/no answer. 

Symphony
Symphony™ Software is a client/server application that is triggered by a MassLynx 
acquisition and allows the automation of one, or several, post-acquisition data 
processing functions in a sequence. It is built with efficiency, flexibility, and  
creativity in mind and enables laboratories to extract maximum value from  
LC-MS instrumentation. 

NuGenesis Lab Management System 
NuGenesis® LMS has multiple points of integration with Masslynx. The Scientific 
Data Management System (SDMS) within NuGenesis LMS provides capabilities 
to manually or automatically capture reports from MassLynx and archive the data 
files generated by the MassLynx application. In addition to the data management 
functionality, NuGenesis LMS Connectors can automate the bi-directional 
communication of sample and result data to MassLynx with laboratory business 
systems like SAP and other commercially available LIMS systems. 

For your local sales office, please visit www.waters.com/contact

Waters Corporation 
34 Maple Street 
Milford, MA 01757 U.S.A. 
T: 1 508 478 2000 
F: 1 508 872 1990 
www.waters.com

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Waters, The Science of What’s Possible, ACQUITY, Empower, HDMS, MassLynx, NuGenesis,  
Progenesis, SYNAPT, UPC2, UPLC, and Xevo are registered trademarks of Waters Corporation. 
ApexTrack, BiopharmaLynx, ChromaLynx, DDA, EPCAS, FractionLynx, i-FIT, IntelliStart, LiveID, 
LockSpray, MarkerLynx, MassFragment, MetaboLynx, NanoLockSpray, OpenLynx, ProfileLynx, 
ProteinLynx, QuanOptimize, Sample Centric, Symphony, TargetLynx, and UniSpray are trademarks  
of Waters Corporation. All other trademarks are the property of their respective owners.

©2017 Waters Corporation. Printed in the U.S.A.  September 2017  720001408EN  LM-SIG