ArticleMolecular & cellular proteomics : MCP2015
Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data.
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 85 papers.
What it found
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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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Who cites it
85 citing papers in PubMed.
- Full-DIA enables complete single-cell proteomics from diaPASEF using deep learning.Genome biology · 2026Article
- xTracer: Integrating chromatogram and mobiligram correlations for untargeted peptide identification in SLIM-based PAMAF data.bioRxiv : the preprint server for biology · 2026Article
- Development of Highly Multiplex Targeted Proteomics Assays in Biofluids Using a Nominal Mass Ion Trap Mass Spectrometer.Molecular & cellular proteomics : MCP · 2026Article
- Data-independent acquisition-based quantitative proteomics in plants.Frontiers in plant science · 2026Review
- Proteogenomic Identification of Annotated and Novel smORFs Via Microprotein Enrichment.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Storing Mass-Spectrometry Data in Simple Databases Enables Flexible and Intuitive Exploration without Time or Space Penalties.Journal of proteome research · 2025Article
- Scoring information integration with statistical quality control enhanced cross-run analysis of data-independent acquisition proteomics data.Communications chemistry · 2025Article
- Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics.Nature communications · 2025Article
- Improving Proteomic Dynamic Range with Multiple Accumulation Precursor Mass Spectrometry.Journal of proteome research · 2025Article
- Carafe enables high qualitybioRxiv : the preprint server for biology · 2025Article
- Unifying the analysis of bottom-up proteomics data with CHIMERYS.Nature methods · 2025Article
- Comprehensive analysis of blood proteome response to necrotic enteritis in broiler chicken.Veterinary research · 2025Article
- Rapid assay development for low input targeted proteomics using a versatile linear ion trap.Nature communications · 2025Article
- TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics.Journal of proteome research · 2025Article
- diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.Nature communications · 2025Article
- Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification.Proteomics · 2025Review
- Automated High-Throughput Biological Sex Identification from Archeological Human Dental Enamel Using Targeted Proteomics.Journal of proteome research · 2024Article
- diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.bioRxiv : the preprint server for biology · 2024Article
- Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins.Microbiome · 2024Article
- Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification.Molecular & cellular proteomics : MCP · 2024Review
25 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
10 authors.
Funding
Abstract
In mass spectrometry-based bottom-up proteomics, data-independent acquisition is an emerging technique because of its comprehensive and unbiased sampling of precursor ions. However, current data-independent acquisition methods use wide precursor isolation windows, resulting in cofragmentation and complex mixture spectra. Thus, conventional database searching tools that identify peptides by interpreting individual tandem MS spectra are inherently limited in analyzing data-independent acquisition data. Here we discuss an alternative approach, peptide-centric analysis, which tests directly for the presence and absence of query peptides. We discuss how peptide-centric analysis resolves some limitations of traditional spectrum-centric analysis, and we outline the unique characteristics of peptide-centric analysis in general.
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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.