ArticleNature communications2023
MSBooster: improving peptide identification rates using deep learning-based features.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 149 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
149 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Mass Spectral Feature Analysis of Ubiquitylated Peptides Provides Insights into Probing the Dark Ubiquitylome.Journal of the American Society for Mass Spectrometry · 2024Pooled it
- pXg: Comprehensive and Reliable Identification of MHC-I Antigens Using De Novo Peptide Sequencing and Immunotranscriptomic Datasets.Methods in molecular biology (Clifton, N.J.) · 2027Article
- MassNet: billion-scale AI-ready mass spectral corpus empowering scalable deep learning in proteomics.Nature methods · 2026Article
- Proteomic analysis of oxidative modifications in human atherosclerotic plaques and control arteries.Redox biology · 2026Article
- Photosensitizer proximity labeling captures the lipid and protein interactomes.Nature chemical biology · 2026Article
- Article
- Improved Protein Identification in Shotgun Proteomics with a Group-Level Extension of the LPGF Model.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
- Article
- Identification of the plant mitochondrial OrfX protein: A mass spectrometry approach.FEBS letters · 2026Article
- Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics.Nature chemistry · 2026Article
- Polyphenol oxidase depletion in Nicotiana benthamiana enhances recombinant protein purification and preserves native protein integrity.The New phytologist · 2026Article
- Beyond Sequence: Posttranslational Remodeling of Antigens in Autoimmunity.Immunological reviews · 2026Review
- Proteogenomic analysis of the differential stability of cardiac protein isoforms.bioRxiv : the preprint server for biology · 2026Article
- Induction of Oxidative Stress on Retinal Pigment Epithelial Cells Triggered a Proangiogenic Environment.International journal of molecular sciences · 2026Article
- Mechanistic Exploration of Half-Sandwich Iridium(III) Anticancer Compounds through Integrated Cellular, Proteomic, and In Vivo Analyses.Journal of medicinal chemistry · 2026Article
- Long-lived mammals contain more phosphorylation sites in the SIRT6 C-terminus that enhance PARP1 interaction and resistance to oxidative stress.GeroScience · 2026Article
- SLC16A6 is a tyrosine transporter for the melanosome.bioRxiv : the preprint server for biology · 2026Article
- Advancing proteomic discovery through optimized multi-stage scoring and deep learning-enhanced open search.Bioinformatics (Oxford, England) · 2026Article
- iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications.Analytical chemistry · 2026Article
89 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments relies on computational algorithms for matching acquired MS/MS spectra against sequences of candidate peptides using database search tools, such as MSFragger. Here, we present a new tool, MSBooster, for rescoring peptide-to-spectrum matches using additional features incorporating deep learning-based predictions of peptide properties, such as LC retention time, ion mobility, and MS/MS spectra. We demonstrate the utility of MSBooster, in tandem with MSFragger and Percolator, in several different workflows, including nonspecific searches (immunopeptidomics), direct identification of peptides from data independent acquisition data, single-cell proteomics, and data generated on an ion mobility separation-enabled timsTOF MS platform. MSBooster is fast, robust, and fully integrated into the widely used FragPipe computational platform.
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What OpenQuestion holds
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.