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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. Bottom-up proteomics - Wikipedia

   en.wikipedia.org/wiki/Bottom-up_proteomics

   There is limited protein sequence coverage by identified peptides, loss of labile PTMs, and ambiguity of the origin for redundant peptide sequences. [8] Recently the combination of bottom-up and top-down proteomics, so called middle-down proteomics, is receiving a lot of attention as this approach not only can be applied to the analysis of large protein fragments but also avoids redundant ...

4. 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.

5. List of protein structure prediction software - Wikipedia

   en.wikipedia.org/wiki/List_of_protein_structure...

   Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.

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. 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.

8. Sequest - Wikipedia

   en.wikipedia.org/wiki/SEQUEST

   The software evaluates protein sequences from a database to compute the list of peptides that could result from each. The peptide's intact mass is known from the mass spectrum, and Sequest uses this information to determine the set of candidate peptides sequences that could meaningfully be compared to the spectrum by including only those near ...

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.