MS-GF+ makes progress towards a universal database search tool for proteomics
Open accessAbstract
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).
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MassIVE searches public datasets using the MS-GF+ search engine with strict criteria to enforce global <1% FDR at the protein level for single-peptide identifications and stricter <0.01% FDR for proteins identified by >2 peptides.
“MassIVE searches public datasets using the MS-GF+ search engine69, also with strict criteria70 to enforce global <1% FDR at the protein level for single-peptide identifications and stricter <0.01% FDR for proteins identified by >2 peptides.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [69]
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- Authors
- Kim, S., & Pevzner, P. A.
- Affiliations
- University of California San Diego (US)
- Corresponding author
- Pevzner, Pavel A.
- Venue
- Nature Communications
- Published
- 2014-10-31
- Volume
- 5
- Issue
- 1
- Pages
- 5277-5277
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC5036525
- OpenAlex
- W2028673251
- Cited by
- 1,098
- References
- 58
- Citations by year
- 2026: 57 · 2025: 84 · 2024: 101 · 2023: 114 · 2022: 86 · 2021: 136 · 2020: 118 · 2019: 95 · 2018: 89 · 2017: 87 · 2016: 86 · 2015: 42 · 2014: 2 · 2013: 1
- FWCI
- 31.11
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Communications (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (P41GM103484)
- National Center for Research Resources (P41RR024851, 1-P41-RR024851)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
- Keywords
- MS-GF+, database searching, tandem mass spectrometry, peptide identification, proteomics software, spectral library search, fragmentation methods, phosphopeptides, phosphoproteomics, alpha-lytic protease, benchmarking
- MeSH terms
- Peptides, Software, Proteomics, Tandem Mass Spectrometry, Search Engine
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