ArticleNature biotechnology2017
Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS.
Article in Nature biotechnology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 141 citations in OpenAlex.
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- Accurate quantification in proteomics with QuantUMS.Nature biotechnology · 2026Article
- Pho-Tip: One-Pot Dephosphorylation for Rapid and Sensitive Analysis of DIA Phosphoproteomics Data.Analytical chemistry · 2026Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- Proteomic Analysis Provides a New Sight Into the CRABP1 Expression in the Pathogenesis of Hirschsprung Disease.Biochemical genetics · 2025Article
- MultiOmicsAgent: Guided Extreme Gradient-Boosted Decision Trees-Based Approaches for Biomarker-Candidate Discovery in Multiomics Data.Journal of proteome research · 2025Article
- PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals.Cell reports methods · 2024Article
- Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.Nature communications · 2024Article
- Computational approaches to identify sites of phosphorylation.Proteomics · 2024Review
- Animal Wellness: The Power of Multiomics and Integrative Strategies: Multiomics in Improving Animal Health.Veterinary medicine international · 2024Review
- A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development.Molecular & cellular proteomics : MCP · 2023Article
- An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells.Nature communications · 2023Article
- Rapid Profiling of Protein Complex Reorganization in Perturbed Systems.Journal of proteome research · 2023Article
- A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology.Biophysics reports · 2023Article
- DeepFLR facilitates false localization rate control in phosphoproteomics.Nature communications · 2023Article
- Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities.Clinical and translational medicine · 2023Article
- Dear-DIAResearch (Washington, D.C.) · 2023Article
- Proteotype coevolution and quantitative diversity across 11 mammalian species.Science advances · 2022Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 5 institutions in 5 countries.
Funding
Abstract
Consistent detection and quantification of protein post-translational modifications (PTMs) across sample cohorts is a prerequisite for functional analysis of biological processes. Data-independent acquisition (DIA) is a bottom-up mass spectrometry approach that provides complete information on precursor and fragment ions. However, owing to the convoluted structure of DIA data sets, confident, systematic identification and quantification of peptidoforms has remained challenging. Here, we present inference of peptidoforms (IPF), a fully automated algorithm that uses spectral libraries to query, validate and quantify peptidoforms in DIA data sets. The method was developed on data acquired by the DIA method SWATH-MS and benchmarked using a synthetic phosphopeptide reference data set and phosphopeptide-enriched samples. IPF reduced false site-localization by more than sevenfold compared with previous approaches, while recovering 85.4% of the true signals. Using IPF, we quantified peptidoforms in DIA data acquired from >200 samples of blood plasma of a human twin cohort and assessed the contribution of heritable, environmental and longitudinal effects on their PTMs.
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