ArticleMolecular & cellular proteomics : MCP2015
Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet.
Article in Molecular & cellular proteomics : MCP, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed.
- Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry-Based Proteomics.Molecular & cellular proteomics : MCP · 2024Review
- Dear-DIAResearch (Washington, D.C.) · 2023Article
- Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data.Journal of proteome research · 2022Article
- Parallel Factor Analysis Enables Quantification and Identification of Highly Convolved Data-Independent-Acquired Protein Spectra.Patterns (New York, N.Y.) · 2020Article
- Avant-garde: an automated data-driven DIA data curation tool.Nature methods · 2020Article
- Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments.Molecular & cellular proteomics : MCP · 2020Article
- Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition.Molecular & cellular proteomics : MCP · 2020Article
- Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools.International journal of molecular sciences · 2018Review
- Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry.Nature communications · 2018Article
- Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial.Molecular systems biology · 2018Review
- Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses.Nature methods · 2017Article
- Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry.Nature communications · 2017Article
- Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides.Molecular & cellular proteomics : MCP · 2016Article
- Technical advances in proteomics: new developments in data-independent acquisition.F1000Research · 2016Review
- Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS.Journal of proteome research · 2015Article
- reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.Journal of the American Society for Mass Spectrometry · 2015Article
- Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows.Analytical chemistry · 2015Article
- Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry.Journal of proteome research · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Proteomics by mass spectrometry technology is widely used for identifying and quantifying peptides and proteins. The breadth and sensitivity of peptide detection have been advanced by the advent of data-independent acquisition mass spectrometry. Analysis of such data, however, is challenging due to the complexity of fragment ion spectra that have contributions from multiple co-eluting precursor ions. We present SWATHProphet software that identifies and quantifies peptide fragment ion traces in data-independent acquisition data, provides accurate probabilities to ensure results are correct, and automatically detects and removes contributions to quantitation originating from interfering precursor ions. Integration in the widely used open source Trans-Proteomic Pipeline facilitates subsequent analyses such as combining results of multiple data sets together for improved discrimination using iProphet and inferring sample proteins using ProteinProphet. This novel development should greatly help make data-independent acquisition mass spectrometry accessible to large numbers of users.
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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.