ArticleNature methods2017
PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data.
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
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Who cites it
94 citing papers in PubMed.
- Accurate quantification in proteomics with QuantUMS.Nature biotechnology · 2026Article
- A label-free microLC-SWATH-MS methodology with immunoaffinity depletion of highly abundant serum proteins for quantitative proteomic comparison of fresh-frozen human normal breast tissue and tumor clinical specimens.Frontiers in molecular biosciences · 2026Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- Data-independent acquisition-based quantitative proteomics in plants.Frontiers in plant science · 2026Review
- Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes.Journal of proteome research · 2025Article
- Liquid Chromatographic and Mass Spectrometric Methods for Quantitative Proteomic Analysis from Single-Cell and Nanogram-Level Samples.Analytical chemistry · 2025Article
- Toward the Development of a Novel Newborn Screening Modality: In-Depth Nontargeted Proteome Analysis of Dried Blood Spots with a Robotic Pipeline Using Low-Cost Iron Powders.Analytical chemistry · 2025Article
- A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data.Nature methods · 2025Article
- Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer.Journal of proteome research · 2025Article
- Unifying the analysis of bottom-up proteomics data with CHIMERYS.Nature methods · 2025Article
- Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.Proteomics · 2025Article
- Determination of Trends Underlying Aspartic Acid Isomerization in Intact Proteins Reveals Unusually Rapid Isomerization of Tau.ACS chemical neuroscience · 2025Article
- High-Density Lipoprotein Lipid and Protein Cargo and Cholesterol Efflux Capacity Before and After Bariatric Surgery.Arteriosclerosis, thrombosis, and vascular biology · 2025Observational
- 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
- Application of artificial intelligence to quantitative structure-retention relationship calculations in chromatography.Journal of pharmaceutical analysis · 2025Review
- Unusually Rapid Isomerization of Aspartic Acid in Tau.bioRxiv : the preprint server for biology · 2024Article
- diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.bioRxiv : the preprint server for biology · 2024Article
- Harnessing Multi-Omics Strategies and Bioinformatics Innovations for Advancing Soybean Improvement: A Comprehensive Review.Plants (Basel, Switzerland) · 2024Review
- SeFilter-DIA: Squeeze-and-Excitation Network for Filtering High-Confidence Peptides of Data-Independent Acquisition Proteomics.Interdisciplinary sciences, computational life sciences · 2024Article
34 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
Data-independent acquisition (DIA) is an emerging mass spectrometry (MS)-based technique for unbiased and reproducible measurement of protein mixtures. DIA tandem mass spectrometry spectra are often highly multiplexed, containing product ions from multiple cofragmenting precursors. Detecting peptides directly from DIA data is therefore challenging; most DIA data analyses require spectral libraries. Here we present PECAN (http://pecan.maccosslab.org), a library-free, peptide-centric tool that robustly and accurately detects peptides directly from DIA data. PECAN reports evidence of detection based on product ion scoring, which enables detection of low-abundance analytes with poor precursor ion signal. We demonstrate the chromatographic peak picking accuracy and peptide detection capability of PECAN, and we further validate its detection with data-dependent acquisition and targeted analyses. Lastly, we used PECAN to build a plasma proteome library from DIA data and to query known sequence variants.
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Registered trials
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