ArticleJournal of proteome research2012
Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification.
Article in Journal of proteome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
42 citing papers in PubMed.
- Advances in the Design and Functionality of a Compact Multi-Reflecting Time-of-Flight Mass Spectrometer.Rapid communications in mass spectrometry : RCM · 2026Article
- Clinical Applications of Phosphoproteomics: Illuminating Cancer Signaling and Enabling Rational Therapeutic Strategies.Cancer science · 2026Review
- Mass Spectrometry-Based Biomarkers in Drug Development.Advances in experimental medicine and biology · 2026Review
- Data-independent acquisition-based quantitative proteomics in plants.Frontiers in plant science · 2026Review
- Mass Spectrometry-Based Biomarkers in Drug Development.Advances in experimental medicine and biology · 2026Review
- Proteomic Profiling of Venoms fromToxins · 2024Article
- Deep representation features from DreamDIACommunications biology · 2021Article
- CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation.Journal of proteome research · 2021Article
- Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling.Journal of proteome research · 2021Article
- Quantitative Mass Spectrometry-Based Proteomics: An Overview.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Application of Proteomics in Sarcoidosis.American journal of respiratory cell and molecular biology · 2020Review
- DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics.Nature communications · 2020Article
- Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results.Journal of proteome research · 2020Article
- Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries.Molecular & cellular proteomics : MCP · 2020Article
- SWATH-MS for metabolomics and lipidomics: critical aspects of qualitative and quantitative analysis.Metabolomics : Official journal of the Metabolomic Society · 2020Review
- Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis.International journal of molecular sciences · 2020Review
- Generating high quality libraries for DIA MS with empirically corrected peptide predictions.Nature communications · 2020Article
- Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition.Molecular & cellular proteomics : MCP · 2020Article
- Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.Journal of the American Society for Mass Spectrometry · 2019Article
- Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry.Nature communications · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Fourier transform-all reaction monitoring (FT-ARM) is a novel approach for the identification and quantification of peptides that relies upon the selectivity of high mass accuracy data and the specificity of peptide fragmentation patterns. An FT-ARM experiment involves continuous, data-independent, high mass accuracy MS/MS acquisition spanning a defined m/z range. Custom software was developed to search peptides against the multiplexed fragmentation spectra by comparing theoretical or empirical fragment ions against every fragmentation spectrum across the entire acquisition. A dot product score is calculated against each spectrum to generate a score chromatogram used for both identification and quantification. Chromatographic elution profile characteristics are not used to cluster precursor peptide signals to their respective fragment ions. FT-ARM identifications are demonstrated to be complementary to conventional data-dependent shotgun analysis, especially in cases where the data-dependent method fails because of fragmenting multiple overlapping precursors. The sensitivity, robustness, and specificity of FT-ARM quantification are shown to be analogous to selected reaction monitoring-based peptide quantification with the added benefit of minimal assay development. Thus, FT-ARM is demonstrated to be a novel and complementary data acquisition, identification, and quantification method for the large scale analysis of peptides.
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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.