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The prevailing experimental method for protein identification is a bottom-up approach, where a protein sample is typically digested with trypsin to form smaller peptides. While most proteins are too large, peptides usually fall within the limited mass range that a typical mass spectrometer can measure.
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 ...
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.
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.
Scientific workflow and data integration system Unix-like: Academic Free: Collaborative project GenePattern: Scientific workflow system that provides access to hundreds of genomic analysis tools Unix-like (public server); Linux, macOS, Windows: MIT: Broad Institute, UC San Diego: Geworkbench: Genomic data integration platform Linux, macOS, Windows
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A scientific workflow is the process of combining data and processes into a configurable, structured set of steps that implement semi-automated computational solutions to a scientific problem. Scientific workflow systems often provide graphical user interfaces to combine different technologies along with efficient methods for using them, and ...
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