MassLynx Mass Spectrometry Software

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, turn to Waters software to simplify interaction with your MS system and retain the ability to perform advanced experiments.

Waters MassLynx™ Software 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 delivers the versatility and flexibility you require.

Transform Data Into Usable Results

To assist with both data acquisition and the transformation of data into usable results, MassLynx Software offers easy-to-use Application Managers that allow you to focus the power of MS on your laboratory's specific tasks.


MassLynx MS Software A fundamental platform to acquire, analyze, manage, and share mass spectrometry information
Quanpedia Quanpedia is an extensible and searchable database for quantitative LC/MS and LC/MS/MS method information. Quanpedia simplifies and accelerates quantitative UPLC/MS/MS analytical method creation.
QCMonitor QCMonitor for MassLynx Software automates “on time” quantitative data quality monitoring to determine whether a QC or blank sample is within tolerances specified by the user.
TrendPlot TrendPlot for MassLynx Software charts long-term system performance. Perform statistical analysis – identify outliers within a sample run, or spot trends in historical data across many sample runs.
TargetLynx For high-throughput targeted quantification and confirmation analyses, complete with a full-range of automatic quality control checks
NeoLynx The NeoLynx Screening Application Manager measures phenylalanine and tyrosine in neonatal blood samples analyzed by LC/MS/MS.
OpenLynx Open Access Provides open access walk-up for LC/UV, LC/MS, LC/MS/MS, and GC/MS operation
FractionLynx Automates sample purification, including the control of fraction collection as well as sample, fraction and data tracking.
ChromaLynx Automate the processing of LC/MS, GC/MS, LC/MS/MS, or GC/MS/MS data allowing for the detection, identification, and semi-quantitative determination of components in complex mixtures.
MassFragment MassFragment is a chemically intelligent structure elucidation tool for the structural assignment of product ions of your known chemical structures.
MetaboLynx XS Rapidly detects the peaks in your LC/MS & LC/MS/MS sample analysis that result from in vitro or in vivo biotransformation.
QuanOptimize The QuanOptimize Application Manager automates MRM (or SIR) method set-up for unattended "multi compound" quantitative LC/MS or LC/MS/MS analyses.
MarkerLynx Processes complex multivariate data from LC/MS, LC/MS/MS, GC/MS, and GC/MS/MS metabonomic and metabolomic studies.
ProfileLynx Automates data processing for chromatography-based tests used in physicochemical property analyses for lead optimization.
POSI±IVE Review qualitative and quantitative TOF data in a single pass with POSI±IVE Software, and report just the quantitative results for positively detected components.
BiopharmaLynx Determines the identity, purity, and stability of biopharmaceutical products from peptide maps or intact proteins.
ProteinLynx Global SERVER (PLGS) A mass-informatics platform for quantitative and qualitative proteomics research and the central analytical platform for Waters proteomics systems.

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