Phoenix Enhancer: an online service/tool for proteomics data mining using clustered spectra

Motivation Spectrum clustering has been proved to enhance proteomics data analysis: some originally unidentified spectra can be potentially identified and individual peptides can also be evaluated to find potentially mis-identifications by using clusters of identified spectra. The Phoenix Enhancer spectrum service/tool provides an infrastructure to perform data analysis on tandem mass spectra and the corresponding peptides against previously identified public data. Based on previously released PRIDE Cluster data and a newly developed pipeline, four functionalities are provided: i) evaluate the original peptide identifications in an individual dataset, to find low confident peptide spectrum matches (PSMs) which could correspond to mis-identifications; ii) provide confidence scores for all originally identified PSMs, to help users to evaluate their quality (complementary to getting a global false discovery rate); iii) identified potentially new PSMs to originally unidentified spectra; and iv) provide a collection of browsing and visualization tools to analyze and export the results. The code is open-source and easy to re-deploy on local computers using Docker containers. Availability The service of Phoenix Enhancer is available at http://enhancer.ncpsb.org. Contact baimingze@gmail.com, hhe@ebi.ac.uk Supplementary information Supplementary data are available at online.