ReviewMolecular systems biology2018
Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial.
Review in Molecular systems biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 491 papers, 1 of them a synthesis that pooled it.
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Who cites it
491 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Exploring Biomarkers in Type 2 Diabetes Mellitus versus Normoglycemia Identified through High-Throughput Proteomics: A Systematic Review and Meta-Analysis.Journal of proteome research · 2026Pooled it
- Preprocessing Large-Scale Proteomics Data.Methods in molecular biology (Clifton, N.J.) · 2027Article
- ProFormer: generalizable classification of single-cell and plasma proteomes using deep learning.Nature communications · 2026Article
- Review
- Scalable clinical proteomics from DNA/RNA extraction flowthroughs enables integrated proteogenomic profiling from a single cancer biopsy.Clinical proteomics · 2026Article
- A Review of Proteomic Studies in Uterine Leiomyosarcoma: Biomarkers, Pathways, and Clinical Potential.Current issues in molecular biology · 2026Review
- Development of a metabolomic LC-QTOF method for bioactive compound production control in plant cell cultures.Analytical and bioanalytical chemistry · 2026Article
- Heat shock protein family D member 1 (HSPD1) modulates ribosome-related pathways and protein synthesis in lung adenocarcinoma.Molecular and cellular biochemistry · 2026Article
- Identification and Validation of Plasma Protein Biomarkers for Abdominal Aortic Aneurysm Using Integrated Proteomics.International journal of molecular sciences · 2026Article
- Investigation of the In Vitro and In Vivo Metabolism and μ-Opioid Receptor Affinity of the Nitazene N-Pyrrolidino Fluetonitazene.Drug testing and analysis · 2026Article
- Understanding Mass Spectrometry: From Ion Generation to Spectral Interpretation.Journal of mass spectrometry : JMS · 2026Article
- Article
- Disruption of hippocampal upstream regulators of mTOR and insulin pathways in Down syndrome with Alzheimer's disease neuropathology: Preliminary observations.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Plasma Proteomics in IgA Nephropathy: From Circulating Biomarkers to Molecular Endotypes.Cells · 2026Review
- DiaReport: reproducible workflow for differential expression analysis and interactive reporting in DIA-based proteomics.Bioinformatics (Oxford, England) · 2026Article
- Proteomics-based insights into mammalian oocyte and early embryo development.Nature cell biology · 2026Review
- Ultrahigh-Throughput Liquid Chromatography with Tandem Mass Spectrometry Method for Targeted Protein Degradation Compound Screening Using the Orbitrap Astral Mass Spectrometer.Journal of proteome research · 2026Article
- Accurate quantification in proteomics with QuantUMS.Nature biotechnology · 2026Article
- Coordination of Cyanobacterial Nitrate Assimilation and Photosynthesis by a Novel PsbO-Interacting Protein PirN.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- JUMPlion improves quantitative DIA proteomics through ion-level recovery of missing values.bioRxiv : the preprint server for biology · 2026Article
431 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many research questions in fields such as personalized medicine, drug screens or systems biology depend on obtaining consistent and quantitatively accurate proteomics data from many samples. SWATH-MS is a specific variant of data-independent acquisition (DIA) methods and is emerging as a technology that combines deep proteome coverage capabilities with quantitative consistency and accuracy. In a SWATH-MS measurement, all ionized peptides of a given sample that fall within a specified mass range are fragmented in a systematic and unbiased fashion using rather large precursor isolation windows. To analyse SWATH-MS data, a strategy based on peptide-centric scoring has been established, which typically requires prior knowledge about the chromatographic and mass spectrometric behaviour of peptides of interest in the form of spectral libraries and peptide query parameters. This tutorial provides guidelines on how to set up and plan a SWATH-MS experiment, how to perform the mass spectrometric measurement and how to analyse SWATH-MS data using peptide-centric scoring. Furthermore, concepts on how to improve SWATH-MS data acquisition, potential trade-offs of parameter settings and alternative data analysis strategies are discussed.
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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.