Universal database search tool for proteomics

By Sangtae Kim, Pavel A. Pevzner. Nature Communications, 2014

1,044 citations recorded by the source corpus.

Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but the software tools to analyse tandem mass spectra are lagging behind. We present a database search tool MS-GF+ that is sensitive (it identifies more peptides than most other database search tools) and universal (it works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols). We benchmark MS-GF+ using diverse spectral data sets: (i) spectra of varying fragmentation methods; (ii) spectra of multiple enzyme digests; (iii) spectra of phosphorylated peptides; and (iv) spectra of peptides with unusual fragmentation propensities produced by a novel alpha-lytic protease. For all these data sets, MS-GF+ significantly increases the number of identified peptides compared with commonly used methods for peptide identifications. We emphasize that although MS-GF+ is not specifically designed for any particular experimental set-up, it improves on the performance of tools specifically designed for these applications (for example, specialized tools for phosphoproteomics). The development of software tools to analyse large mass spectrometry data sets lags behind the increase in diversity of the data. Here the authors develop MS-GF+, a database search tool that outperforms other popular tools in identifying peptides from a variety of data sets.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/e45a8d7176bd738c1e63de1f6791a88e704f8b4b

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Citations in the corpus

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition (2016, background): “Among many other options, data sets can be reanalyzed by spectral library search (MSPLIT (21)), standard database search (MS-GF+ (22)), proteogenomics database search (Enosi (23)), spectral networks (24) and MODa (25) blind search for unexpected modifications, and spectral library search of DIA data”
2016 update of the PRIDE database and its related tools (2015, background): “This includes, among others, MS-GF+ (42), Mascot (Matrix Science, from version 2.4), ProteinPilot (AB SCIEX), PEAKS (Bioinformatics Solutions Inc), Scaffold (Proteome Software), MyriMatch (43) and PeptideShaker (44) and recently X!”