ArticleNucleic acids research2019
Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed, 108 citations in OpenAlex.
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- Less missing values-evaluation of proteomics workflows for the quantification of (small) proteins.microLife · 2026Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- AIRPred: A Deep Learning Model Predictor for Peptide Intensity Ratios in Cross-Linking Mass Spectrometry Improves Cross-Link Spectrum Matching.Analytical chemistry · 2025Article
- Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring.Journal of proteome research · 2025Article
- TIMSJournal of proteome research · 2025Article
- Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity.Nature communications · 2024Article
- Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification.Molecular & cellular proteomics : MCP · 2024Review
- Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel.Nature protocols · 2024Article
- Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MSNature communications · 2024Article
- Identification and Targeted Quantification of Endogenous Neuropeptides in the Nematode Caenorhabditis elegans Using Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Making MS Omics Data ML-Ready: SpeCollate Protocols.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Bioinformatics Pipeline for Processing Single-Cell Data.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Deep Learning-Assisted Analysis of Immunopeptidomics Data.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Data-Independent Acquisition Peptidomics.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Updated MS²PIP web server supports cutting-edge proteomics applications.Nucleic acids research · 2023Article
- 2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study.Journal of biomolecular techniques : JBT · 2023Article
- Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future.Proteomics · 2023Article
- Integrated View of Baseline Protein Expression in Human Tissues.Journal of proteome research · 2023Article
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Authors and funding
3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
MS²PIP is a data-driven tool that accurately predicts peak intensities for a given peptide's fragmentation mass spectrum. Since the release of the MS²PIP web server in 2015, we have brought significant updates to both the tool and the web server. In addition to the original models for CID and HCD fragmentation, we have added specialized models for the TripleTOF 5600+ mass spectrometer, for TMT-labeled peptides, for iTRAQ-labeled peptides, and for iTRAQ-labeled phosphopeptides. Because the fragmentation pattern is heavily altered in each of these cases, these additional models greatly improve the prediction accuracy for their corresponding data types. We have also substantially reduced the computational resources required to run MS²PIP, and have completely rebuilt the web server, which now allows predictions of up to 100 000 peptide sequences in a single request. The MS²PIP web server is freely available at https://iomics.ugent.be/ms2pip/.
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