Bo’s paper PepQuery2 democratizes public MS proteomics data for rapid peptide searching has been published in...

Bo’s paper PepQuery2 democratizes public MS proteomics data for rapid peptide searching has been published in Nature Communications. One of the most important milestones in proteomics is the Amsterdam Principles, which require mandatory raw MS/MS data deposition to promote broad reuse of the data. However, because of the challenges involved in understanding, downloading, analyzing, and interpreting MS/MS data, investigation and reuse of these public data are largely restricted to computational proteomics researchers. By enabling rapid identification of any known or novel peptide sequences of interest in any local or publicly available MS-based proteomics datasets in a targeted manner, PepQuery2 provides a practical solution that makes public MS/MS data easily useful to the general research community. Both the command line version and the web version of PepQuery2 are available at http://www.pepquery.org. The source code of PepQuery2 is available at https://github.com/bzhanglab/PepQuery.