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Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry Proteomics software. Announced the shipment of Waters MassLynx 4.1 Software, its market-leading solution for the company's line of mass spectrometers. MassLynx Software has been enhanced and reconfigured to facilitate high-performance quantification and qualitative analysis so that users can process and review resultsand. Waters MassLynx MassLynx is the data acquisition software for Waters mass spectrometers. There are several options available for processing Waters raw data into peak lists for searching with Mascot. Is the Waters software environment for proteomics project management, protein quantification, and protein identification and characterization.