Bo’s paper PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations has been published in Genome Research. Congratulations, Bo! PepQuery is a peptide-centric search engine that allows quick and easy proteomic validation of genomic alterations without customized database construction. Next generation sequencing-based genomic studies continuously identify new genomic alterations that may lead to novel protein sequences, which are attractive candidates for disease biomarkers and therapeutic targets after proteomic validation. The popular approach for proteomic validation requires customized database construction and a full evaluation of all possible spectrum-peptide pairs, which is time-consuming. We implemented PepQuery as both stand-alone and web-based applications. The stand-alone version supports batch analysis and user-provided MS/MS data. The web version provides access to more than half a billion MS/MS spectra from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and other cancer proteomic studies, making MS/MS data directly available and useful to scientists outside the proteomics community. PepQuery can be accessed at http://www.pepquery.org.
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