ArticleJournal of proteome research2022
Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?
Article in Journal of proteome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 2 of them syntheses that pooled it.
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.
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
59 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Properties, Origin, and Consistency of Truncated Proteoforms Across Top-Down Proteomic Studies.Molecular & cellular proteomics : MCP · 2025Pooled it
- Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments.Nature methods · 2023Guideline
- 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
- Beyond sarcomere genetics: proteomic insights into hypertrophic cardiomyopathy.Biophysical reviews · 2026Review
- Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.Nature communications · 2026Article
- Proteoforms as the true units of physiological function.European journal of applied physiology · 2026Review
- Development of Highly Multiplex Targeted Proteomics Assays in Biofluids Using a Nominal Mass Ion Trap Mass Spectrometer.Molecular & cellular proteomics : MCP · 2026Article
- Global Proteoform Alterations Across Multiple Cellular Compartments Underlie Obstructive Hypertrophic Cardiomyopathy.Circulation. Heart failure · 2025Article
- Top-Down Thermal Proteome Profiling (TD-TPP) for Functional Characterization of the Intact Proteoforms in Complex Samples.Journal of mass spectrometry : JMS · 2025Article
- Sample preparation and cleanup methods for clinical top-down proteomics.Expert review of proteomics · 2025Review
- Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome.NPJ biofilms and microbiomes · 2025Article
- scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data.Genome biology · 2025Article
- Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome.Nature communications · 2025Article
- Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer.Journal of proteome research · 2025Article
- MultiOmicsAgent: Guided Extreme Gradient-Boosted Decision Trees-Based Approaches for Biomarker-Candidate Discovery in Multiomics Data.Journal of proteome research · 2025Article
- Improved quantitative accuracy in data-independent acquisition proteomics via retention time boundary imputation.bioRxiv : the preprint server for biology · 2025Article
- Peptide Property Prediction for Mass Spectrometry Using AI: An Introduction to State of the Art Models.Proteomics · 2025Review
- Normalized and Directional Interplay Scoring for the Interrogation of Proteoform Data.Journal of proteome research · 2025Article
- A Proteomic Signature for Human Papillomavirus-Associated Oropharyngeal Squamous Cell Carcinoma Predicts Patients at High Risk of Recurrence.Cancer research communications · 2025Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Bottom-up proteomics provides peptide measurements and has been invaluable for moving proteomics into large-scale analyses. Commonly, a single quantitative value is reported for each protein-coding gene by aggregating peptide quantities into protein groups following protein inference or parsimony. However, given the complexity of both RNA splicing and post-translational protein modification, it is overly simplistic to assume that all peptides that map to a singular protein-coding gene will demonstrate the same quantitative response. By assuming that all peptides from a protein-coding sequence are representative of the same protein, we may miss the discovery of important biological differences. To capture the contributions of existing proteoforms, we need to reconsider the practice of aggregating protein values to a single quantity per protein-coding gene.
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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.