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  2. List of mass spectrometry software - Wikipedia

    en.wikipedia.org/wiki/List_of_mass_spectrometry...

    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

  3. Mascot (software) - Wikipedia

    en.wikipedia.org/wiki/Mascot_(software)

    Mascot identifies proteins by interpreting mass spectrometry data. 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 ...

  4. Bottom-up proteomics - Wikipedia

    en.wikipedia.org/wiki/Bottom-up_proteomics

    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 ...

  5. Galaxy (computational biology) - Wikipedia

    en.wikipedia.org/wiki/Galaxy_(computational_biology)

    Galaxy is a scientific workflow system. These systems provide a means to build multi-step computational analyses akin to a recipe. They typically provide a graphical user interface [6] for specifying what data to operate on, what steps to take, and what order to do them in. Galaxy is also a data integration platform for biological data.

  6. Skyline (software) - Wikipedia

    en.wikipedia.org/wiki/Skyline_(software)

    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. It contains a graphical user interface to display chromatographic data for individual peptide or small molecule analytes.

  7. Apache Taverna - Wikipedia

    en.wikipedia.org/wiki/Apache_Taverna

    The Taverna workflow engine was also available separately, as a Java API, command line tool or as a server. Taverna was used by users in many domains, such as bioinformatics , [ 9 ] [ 10 ] cheminformatics , [ 11 ] medicine , astronomy , [ 12 ] social science , music , and digital preservation .

  8. Trans-Proteomic Pipeline - Wikipedia

    en.wikipedia.org/wiki/Trans-Proteomic_Pipeline

    The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, [2] ProteinProphet, [3] ASAPRatio, XPRESS and Libra.

  9. List of bioinformatics software - Wikipedia

    en.wikipedia.org/.../List_of_bioinformatics_software

    List of protein structure prediction software; Category:Molecular dynamics software; Structural alignment software; Other. Compression of genomic sequencing data; Bioinformatics workflow management system; List of genetic engineering software; List of systems biology visualization software; List of systems biology modelling software; 2D gel ...

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