Allows to manage and analyse Liquid chromatography coupled to mass spectrometry (LC-MS) data. OpenMS is a programming library and tool collection integrated into full-featured workflow systems, such as KNIME, Galaxy and WS-PGRADE, to facilitate bioinformatics research in the field of MS on all levels. The software provides pre-built and ready-to-use tools for analysis of both proteomics and non-targeted metabolomics data.
An R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows and data-dependent, targeted and data-independent spectral acquisition. It takes as input identified and quantified spectral peaks, and outputs a list of differentially abundant peptides or proteins, or summaries of peptide or protein relative abundance. MSstats relies on a flexible family of linear mixed models.
A proteomics software that allows analysis of LC-MS/MS DIA (data independent acquisition) data. OpenSWATH was designed and optimized to work with profile data. While the software will run on centroided data, depending on the pre-processing applied, the quality of the chromatograms suffers and the results will be of lower quality.
Professional software that enables fully automated, fast and accurate signal processing of SWATH and DIA data sets (HRM-MS). HRM-MS is the next generation targeted proteomics technology invented at Biognosys that enables reproducible and precise quantification of 1000s of proteins in a single instrument run with data independent acquisition (DIA).
Allows users to acquire, analyze, manage, and share mass spectrometry information. MassLynx MS Software permits the conversion of sample data into valuable knowledge. This application can control Waters mass spectrometry system, from sample and solvent management components to mass spectrometer and auxiliary detectors. It can acquire nominal mass, exact mass, tandem mass spectrometry (MS/MS) and exact mass MS/MS data.