Publicly Available Software

The facility develops many tools to assist in proteomic data analysis. Most of these are developed and released as part of the package Protein Prospector Over a million searches using this package of tools are preformed through the public website every year.

Among the most popular program in Protein Prospector are a program for theoretical digestion of proteins, MS-Digest; a program for theoretical fragmentation and annotation of MSMS spectra, MS-Product and a program for plotting theoretical isotope distributions of molecules, MS-Isotope.

However, many of the most exciting features of this package are designed for the batch analysis of MSMS spectra. The software is powerful for the analysis of regular peptides(1) and excels at analyzing ETD data(2). The software allows discovery of unexpected modifications using mass modification searching, and this has been adapted to allow analysis of cross-linked peptides, producing more reliable results than alternative software(3). The software was also shown in a community study to be top performing for the analysis of glycopeptide data(4).

The Protein Prospector software is freely available through the public website. Licensed versions of Protein Prospector binaries and source code are freely available. Please contact ppadmin@cgl.ucsf.edu for more information.

References
1. Chalkley RJ, Baker PR, Medzihradszky KF, Lynn AJ, Burlingame AL. In-depth Analysis of Tandem Mass Spectrometry Data from Disparate Instrument Types. Mol Cell Proteomics. 2008;7(12):2386-98.[pubmed]
2. Baker PR, Medzihradszky KF, Chalkley RJ. Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state- and sequence-dependent scoring. Mol Cell Proteomics. 2010;9(9):1795-1803.[pubmed]
3. Trnka MJ, Baker PR, Robinson PJ, Burlingame AL, Chalkley RJ. Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics. 2014;13(2):420-34.[pubmed]
4. Kawahara et al. Nat Methods 2021 18(11):1304-1316.[pubmed]