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MetaMorpheus is a proteomics search software developed at the University of Wisconsin-Madison with integrated calibration, post-translational modification discovery, bottom-up and top-down proteomics search, cross-linking mass spectrometry (XL-MS) search, proteogenomic search, and label-free quantification (LFQ) capabilities. [7] MSFragger Freeware
Essentially, bottom-up proteomics is a relatively simple and reliable means of determining the protein make-up of a given sample of cells, tissues, etc. [5] In bottom-up proteomics, the crude protein extract is enzymatically digested, followed by one or more dimensions of separation of the peptides by liquid chromatography coupled to mass ...
Legacy software versions exist for Tru64, Irix, AIX, Solaris, Microsoft Windows NT4 and Microsoft Windows 2000. Mascot has been available as a free service on the Matrix Science website since 1999 and has been cited in scientific literature over 5,000 times. Matrix Science still continues to work on improving Mascot’s functionality.
Skyline is an open source software for targeted proteomics [1] [2] and metabolomics [3] data analysis. It runs on Microsoft Windows and supports the raw data formats from multiple mass spectrometric vendors.
Targeted proteomics using SRM and data-independent acquisition methods are often considered alternatives to shotgun proteomics in the field of bottom-up proteomics. While shotgun proteomics uses data-dependent selection of precursor ions to generate fragment ion scans, the aforementioned methods use a deterministic method for acquisition of ...
Galaxy [2] is a scientific workflow, data integration, [3] [4] and data and analysis persistence and publishing platform that aims to make computational biology and other scientific disciplines accessible to research scientists that do not have computer programming or systems administration experience.
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ProteoWizard is a set of open-source, cross-platform tools and libraries for proteomics data analyses. [1] [2] It provides a framework for unified mass spectrometry data file access and performs standard chemistry and LCMS dataset computations. Specifically, it is able to read many of the vendor-specific, proprietary formats and converting the ...