ArticleJournal of proteome research2021
Peptide Correlation Analysis (PeCorA) Reveals Differential Proteoform Regulation.
Article in Journal of proteome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed, 44 citations in OpenAlex.
- ProteoForge: An Imputation-Aware Framework for Differential Proteoform Discovery in Bottom-Up Proteomics.Journal of proteome research · 2026Article
- Aggregation Methods for Quantifying PTM and Structural Changes in Bottom-Up Proteomics.Journal of proteome research · 2026Article
- Top-Down Proteomics: Why and When?Proteomics · 2025Article
- scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data.Genome biology · 2025Article
- A Proteomic Signature for Human Papillomavirus-Associated Oropharyngeal Squamous Cell Carcinoma Predicts Patients at High Risk of Recurrence.Cancer research communications · 2025Article
- Revisiting the Effect of Trypsin Digestion Buffers on Artificial Deamidation.Journal of the American Society for Mass Spectrometry · 2025Article
- Relative quantification of proteins and post-translational modifications in proteomic experiments with shared peptides: a weight-based approach.Bioinformatics (Oxford, England) · 2025Article
- Functional proteoform group deconvolution reveals a broader spectrum of ibrutinib off-targets.Nature communications · 2025Article
- Quantitative Top-down Proteomics Revealed Kinase Inhibitor-Induced Proteoform-Level Changes in Cancer Cells.Journal of proteome research · 2025Article
- Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst.Journal of proteome research · 2024Article
- Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer.Journal of biomolecular techniques : JBT · 2024Article
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.ACS measurement science au · 2024Review
- Alternative proteoforms and proteoform-dependent assemblies in humans and plants.Molecular systems biology · 2024Article
- Instrumentation at the Leading Edge of Proteomics.Analytical chemistry · 2024Review
- Analysis and visualization of quantitative proteomics data using FragPipe-Analyst.bioRxiv : the preprint server for biology · 2024Article
- Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics.Nature biomedical engineering · 2024Article
- Article
- SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics.Nature communications · 2023Article
- Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis.Nature communications · 2023Article
- Proteoforms feel the heat.Nature chemical biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Shotgun proteomics techniques infer the presence and quantity of proteins using peptide proxies produced by cleavage of the proteome with a protease. Most protein quantitation strategies assume that multiple peptides derived from a protein will behave quantitatively similar across treatment groups, but this assumption may be false due to (1) heterogeneous proteoforms and (2) technical artifacts. Here we describe a strategy called peptide correlation analysis (PeCorA) that detects quantitative disagreements between peptides mapped to the same protein. PeCorA fits linear models to assess whether a peptide's change across treatment groups differs from all other peptides assigned to the same protein. PeCorA revealed that ∼15% of proteins in a mouse microglia stress data set contain at least one discordant peptide. Inspection of the discordant peptides shows the utility of PeCorA for the direct and indirect detection of regulated post-translational modifications (PTMs) and also for the discovery of poorly quantified peptides. The exclusion of poorly quantified peptides before protein quantity summarization decreased false-positives in a benchmark data set. Finally, PeCorA suggests that the inactive isoform of prothrombin, a coagulation cascade protease, is more abundant in plasma from COVID-19 patients relative to non-COVID-19 controls. PeCorA is freely available as an R package that works with arbitrary tables of quantified peptides.
Indexed as
Identifiers
What OpenQuestion holds
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.