MassLynx Mass Spectrometry Software

MassLynx Mass Spectrometry Software

Our well-established MassLynx software package delivers market-leading versatility and flexibility for all application areas. 

Our well-established MassLynx software package delivers market-leading versatility and flexibility for all application areas. 
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MassLynx was first pioneered to simplify interaction with mass spectrometry (MS) and has continually improved to meet changing customer needs. The result: a market-leading software solution that allows users to best leverage their MS system and harness real-time intelligence, ensure MS system performance, and more quickly convert sample data into valuable knowledge. With development largely driven by input from our extensive user base, MassLynx provides the fundamental platform to acquire, analyze, manage, and share mass spectrometry information.

MassLynx Software features a 21 CFR Part 11-compatible security including file encryption, audit log, and secure archival/retrieval technology with flexible security policies to meet your lab requirements. Waters also offers excellent service and support to get the system up and running – for on-time results without the stress.


Perform quantitative mass spectrometry analysis with MassLynx Quantitation Applications, mass spec software offerings include TargetLynx XS, Quanpedia, QCMonitor, QuanOptimize, TrendPlot, and MassLynx Skyline Interface.

Perform open access, walk-up targeted MS analyses for LC-UV, LC-MS instruments with MassLynx Mass Detection Applications, OpenLynx Open Access and FractionLynx, TargetLynx XS.

Identify and characterize all of your lab samples with MassLynx High-Resolution Applications from Waters MassLynx MS Software solutions, designed for High-Resolution Mass Spectrometry data management.

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MassLynx Mass Spectrometry Software FAQs

How does MassLynx simplify the operation of mass spectrometry systems?
MassLynx was developed to make mass spectrometry more accessible and manageable for users at all levels of expertise. Its intuitive interface streamlines system setup, method development, data acquisition, and analysis, reducing the complexity often associated with mass spectrometry workflows. The software provides automated system checks, real-time status updates, and flexible control over acquisition parameters, helping users efficiently manage instruments and data. Additionally, MassLynx includes customizable templates and automated features for tasks like tuning, calibration, and quantitation, which minimizes manual intervention and boosts productivity.

Is MassLynx Software compliant with 21 CFR Part 11?
Yes, MassLynx is fully compatible with 21 CFR Part 11 regulatory requirements, making it suitable for use in regulated laboratory environments. The software includes built-in features that support electronic records and signatures, secure user authentication, and access control. File encryption, secure archival and retrieval, and comprehensive audit trails ensure data integrity and traceability throughout the analytical process. Flexible security policy settings allow laboratories to tailor compliance protocols to meet specific internal or regulatory standards. These capabilities help ensure that MassLynx can be confidently deployed in GMP, GLP, and other compliance-driven environments where adherence to FDA and international data standards is essential.

Can MassLynx manage and archive large sets of MS data securely?
Yes, MassLynx includes robust tools for managing, securing, and archiving large volumes of mass spectrometry data. It features secure file encryption and structured data storage that supports long-term retention and rapid retrieval of analytical results. The software's built-in archival and recovery tools help ensure that critical datasets are preserved and accessible when needed, even in high-throughput environments. Audit logs track all changes to files and workflows, supporting compliance and data integrity. MassLynx can be configured to work with centralized data repositories or external storage systems, offering flexible options for secure data management across single labs or enterprise-wide installations.