ArticleNature protocols2015
Building high-quality assay libraries for targeted analysis of SWATH MS data.
Article in Nature protocols, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 161 papers, 1 of them a synthesis that pooled it.
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Who cites it
161 citing papers in PubMed, 1 synthesis or guideline pooled it, 330 citations in OpenAlex.
- Recent Advances in Proteomics-Based Approaches to Studying Age-Related Macular Degeneration: A Systematic Review.International journal of molecular sciences · 2022Pooled it
- Trial
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- Clinical peptidomics for respiratory diseases: matrices, workflows, and translation towards treatable traits, with a focus on COPD.Clinical proteomics · 2026Review
- A Labrador PeptideAtlas and DIA spectral assay library - resources for proteomics research in dogs.Scientific data · 2026Article
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- Less missing values-evaluation of proteomics workflows for the quantification of (small) proteins.microLife · 2026Article
- Human myocardial-derived highly proliferative cells improve cardiac remodeling after myocardial infarction in mice.The Journal of pharmacology and experimental therapeutics · 2025Article
- Depletion-dependent activity-based protein profiling using SWATH/DIA-MS detects serine hydrolase lipid remodeling in lung adenocarcinoma progression.Nature communications · 2025Article
- Recombinant Protein Spectral Library (rPSL) DIA-MS method improves identification and quantification of low-abundance cancer-associated and kynurenine pathway proteins.Communications chemistry · 2025Article
- Proteomic Insights into IgA Nephropathy: A Comprehensive Analysis of Differentially Expressed Proteins in the Kidney.ACS omega · 2025Article
- [New methods at the transition from research to routine diagnostics].Pathologie (Heidelberg, Germany) · 2025Article
- Quantification of intracellular influenza A virus protein dynamics in different host cells after seed virus adaptation.Applied microbiology and biotechnology · 2025Article
- Deep proteome profiling of metabolic dysfunction-associated steatotic liver disease.Communications medicine · 2025Article
- TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics.Journal of proteome research · 2025Article
- SWATH-MS insights on sodium butyrate effect on mAbs production and redox homeostasis in CHO cells.AMB Express · 2024Article
- Advances in omics data for eosinophilic esophagitis: moving towards multi-omics analyses.Journal of gastroenterology · 2024Review
- Temporal insights into molecular and cellular responses during rAAV production in HEK293T cells.Molecular therapy. Methods & clinical development · 2024Article
- Proteomics Studies on Extracellular Vesicles Derived from Glioblastoma: Where Do We Stand?International journal of molecular sciences · 2024Review
101 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors at 7 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Targeted proteomics by selected/multiple reaction monitoring (S/MRM) or, on a larger scale, by SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) typically relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of crucial importance for the performance of the methods. Here we present a detailed protocol that has been successfully used to build high-quality, extensive reference libraries supporting targeted proteomics by SWATH MS. We describe each step of the process, including data acquisition by discovery proteomics, assertion of peptide-spectrum matches (PSMs), generation of consensus spectra and compilation of MS coordinates that uniquely define each targeted peptide. Crucial steps such as false discovery rate (FDR) control, retention time normalization and handling of post-translationally modified peptides are detailed. Finally, we show how to use the library to extract SWATH data with the open-source software Skyline. The protocol takes 2-3 d to complete, depending on the extent of the library and the computational resources available.
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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.