ArticleNature communications2014
MS-GF+ makes progress towards a universal database search tool for proteomics.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 608 papers, 2 of them syntheses that pooled it.
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Who cites it
608 citing papers in PubMed, 2 syntheses or guidelines pooled it, 1,176 citations in OpenAlex.
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- Comprehensive proteomics and meta-analysis of COVID-19 host response.Nature communications · 2023Pooled it
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- Characterization of aliA and aliB deletion mutants reveals a dominant role of AliA in Haloferax volcanii lipoprotein lipidation.The Journal of biological chemistry · 2026Article
- Carbon source-driven metabolic and regulatory remodeling defines phenomic states in Lipomyces starkeyi.Scientific reports · 2026Article
- DigestedProteinDB: A Compact and Scalable Key-Value Database for In Silico Peptide Digestion and Mass-Based Search.Journal of proteome research · 2026Article
- Instrument-Software Synergy in Proteomics: Systematic Evaluation across Mass Spectrometry Platforms, Search Engines, and Rescoring Methods.Journal of proteome research · 2026Article
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- Cellular signaling within aged skeletal muscle reveals a dysregulated stress-induced remodeling response following volumetric muscle loss in female mice.Physiological reports · 2026Article
- Repurposing the liquid-based Pap test for the detection of ovarian cancer protein biomarkers.Clinical proteomics · 2026Article
- Uncovering functional variants using a high-efficiency PE3-based screening platform.Science advances · 2026Article
- A chromosome-level assembly of the alpine snow alga Chloromonas typhlos.Scientific data · 2026Article
- pAnno: a comprehensive, precise, and fast proteogenomic workflow for the discovery of novel coding regions.Genome biology · 2026Article
- Bioengineered algal lipids enriched in structured medium- and long-chain triacylglycerols, linoleate, andbioRxiv : the preprint server for biology · 2026Article
- MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing.Bioinformatics (Oxford, England) · 2026Article
- A Framework for Database Search with AI Models in Mass Spectrometry-Based Proteomics.Journal of proteome research · 2026Review
548 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.