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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.


A fundamental platform to acquire, analyze, manage, and share mass spectrometry information
For high-throughput targeted quantification and confirmation analyses, complete with a full-range of automatic quality control checks
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.
Automates sample purification, including the control of fraction collection as well as sample, fraction and data tracking.
Provides open access walk-up for LC/UV, LC/MS, LC/MS/MS, and GC/MS operation
Determines the identity, purity, and stability of biopharmaceutical products from peptide maps or intact proteins.
Processes complex multivariate data from LC/MS, LC/MS/MS, GC/MS, and GC/MS/MS metabonomic and metabolomic studies.
MassFragment is a chemically intelligent structure elucidation tool for the structural assignment of product ions of your known chemical structures.
The QuanOptimize Application Manager automates MRM (or SIR) method set-up for unattended "multi compound" quantitative LC/MS or LC/MS/MS analyses.
Automates data processing for chromatography-based tests used in physicochemical property analyses for lead optimization.
Rapidly detects the peaks in your LC/MS & LC/MS/MS sample analysis that result from in vitro or in vivo biotransformation.
The NeoLynx Screening Application Manager measures phenylalanine and tyrosine in neonatal blood samples analyzed by LC/MS/MS.
A Mass-Informatics platform for quantitative and qualitative proteomics research and the central analytical platform for Waters proteomics systems.

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