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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 [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.

6. Shotgun proteomics - Wikipedia

   en.wikipedia.org/wiki/Shotgun_proteomics

   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 ...

7. 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.

8. Dotmatics - Wikipedia

   en.wikipedia.org/wiki/Dotmatics

   Studies is a screening data management tool that allows creation, capture, analysis, and storage of chemical, biological, and ad hoc research data. Studies notebook, a Web-based Electronic lab notebook that supports chemistry, biology, and ad hoc research. It combines a web-based platform with intellectual property protection tools.

9. PEAKS - Wikipedia

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

   PEAKS Q is an add-on tool for protein quantification, supporting label (ICAT, iTRAQ, SILAC, TMT, 018, etc.) and label free techniques. SPIDER is a sequence tag based search tool within PEAKS, which deals with the possible overlaps between the de novo sequencing errors and the homology mutations.