ArticleNature methods2019
Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning.
Article in Nature methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 443 papers, 2 of them syntheses that pooled it.
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Who cites it
443 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Progress and trends on machine learning in proteomics during 1997-2024: a bibliometric analysis.Frontiers in medicine · 2025Pooled 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
- Evaluating the mechanism of action behind controlled hypothermic preservation of donor hearts: A randomized pilot study.The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation · 2025Trial
- Elevation of the mechanically-sensitive e protein emerin links nuclear mechanotransduction to tau-induced cytoskeletal remodeling in neurons.Nucleus (Austin, Tex.) · 2026Article
- Retinal proteomics in neurodegeneration: Insights into ocular and brain disorders.Neural regeneration research · 2026Article
- Integration of artificial intelligence and multi-omics for precision medicine.Functional & integrative genomics · 2026Review
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- Improved Protein Identification in Shotgun Proteomics with a Group-Level Extension of the LPGF Model.Journal of proteome research · 2026Article
- Article
- Beyond Sequence: Posttranslational Remodeling of Antigens in Autoimmunity.Immunological reviews · 2026Review
- Article
- Deep Learning Prediction of O-Glycopeptide Tandem Mass Spectra Enhances O-Glycoproteomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- PLCγ2 deficiency compromises systemic immune tolerance and erodes myelin homeostasis while enhancing oxidative metabolism in the mouse brain.bioRxiv : the preprint server for biology · 2026Article
- AlphaDIA enables DIA transfer learning for feature-free proteomics.Nature biotechnology · 2026Article
- Foundation model enables interpretable open and error-tolerant searching for mass spectrometry-based proteomics.Bioinformatics (Oxford, England) · 2026Article
- iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications.Analytical chemistry · 2026Article
- Revisiting resonance-excitation collision-induced dissociation for data-independent acquisition.bioRxiv : the preprint server for biology · 2026Article
- Timed secreted proteomes reveal regulation of hepatokines by the liver circadian clock.Nature communications · 2026Article
- Noncanonical Transcription and Splicing Shape the Colorectal Cancer Immunopeptidome in MSI and MSS Tumors.Molecular & cellular proteomics : MCP · 2026Article
- Prioritizing peptides for targeted mass spectrometry experiments using deep learning.bioRxiv : the preprint server for biology · 2026Article
383 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In mass-spectrometry-based proteomics, the identification and quantification of peptides and proteins heavily rely on sequence database searching or spectral library matching. The lack of accurate predictive models for fragment ion intensities impairs the realization of the full potential of these approaches. Here, we extended the ProteomeTools synthetic peptide library to 550,000 tryptic peptides and 21 million high-quality tandem mass spectra. We trained a deep neural network, termed Prosit, resulting in chromatographic retention time and fragment ion intensity predictions that exceed the quality of the experimental data. Integrating Prosit into database search pipelines led to more identifications at >10× lower false discovery rates. We show the general applicability of Prosit by predicting spectra for proteases other than trypsin, generating spectral libraries for data-independent acquisition and improving the analysis of metaproteomes. Prosit is integrated into ProteomicsDB, allowing search result re-scoring and custom spectral library generation for any organism on the basis of peptide sequence alone.
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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.