ArticleJournal of proteome research2013
The state of the human proteome in 2012 as viewed through PeptideAtlas.
Article in Journal of proteome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 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
58 citing papers in PubMed.
- MassNet: billion-scale AI-ready mass spectral corpus empowering scalable deep learning in proteomics.Nature methods · 2026Article
- Digital Immunoassays for Sensitive Quantification of Blood Biomarkers Using Solid-State Nanopores.ACS nano · 2026Article
- Discovery of peptides as key regulators of metabolic and cardiovascular crosstalk.Cell reports · 2025Review
- On the Roles of Protein Intrinsic Disorder in the Origin of Life and Evolution.Life (Basel, Switzerland) · 2024Review
- Using Linear Motif Database Resources to Identify SH2 Domain Binders.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Pathway Analysis for Cancer Research and Precision Oncology Applications.Advances in experimental medicine and biology · 2022Article
- Targeted Selected Reaction Monitoring Verifies Histology Specific Peptide Signatures in Epithelial Ovarian Cancer.Cancers · 2021Article
- Zooming into the Dark Side of Human Annexin-S100 Complexes: Dynamic Alliance of Flexible Partners.International journal of molecular sciences · 2020Review
- Delineation of hypoxia-induced proteome shifts in osteosarcoma cells with different metastatic propensities.Scientific reports · 2020Article
- New technologies to analyse protein function: an intrinsic disorder perspective.F1000Research · 2020Review
- Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data.Journal of proteome research · 2019Review
- Multi-functionality of proteins involved in GPCR and G protein signaling: making sense of structure-function continuum with intrinsic disorder-based proteoforms.Cellular and molecular life sciences : CMLS · 2019Review
- The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane Proteins.The Journal of membrane biology · 2019Review
- Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources.Briefings in bioinformatics · 2019Review
- A Systematic Investigation of the Malignant Functions and Diagnostic Potential of the Cancer Secretome.Cell reports · 2019Article
- Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function.Journal of proteome research · 2018Article
- A Quantitative Model for BicD2/Cargo Interactions.Biochemistry · 2018Article
- Assembling the Community-Scale Discoverable Human Proteome.Cell systems · 2018Article
- The Omics Revolution Continues: The Maturation of High-Throughput Biological Data Sources.Yearbook of medical informatics · 2018Review
- AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation.Molecular & cellular proteomics : MCP · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The Human Proteome Project was launched in September 2010 with the goal of characterizing at least one protein product from each protein-coding gene. Here we assess how much of the proteome has been detected to date via tandem mass spectrometry by analyzing PeptideAtlas, a compendium of human derived LC-MS/MS proteomics data from many laboratories around the world. All data sets are processed with a consistent set of parameters using the Trans-Proteomic Pipeline and subjected to a 1% protein FDR filter before inclusion in PeptideAtlas. Therefore, PeptideAtlas contains only high confidence protein identifications. To increase proteome coverage, we explored new comprehensive public data sources for data likely to add new proteins to the Human PeptideAtlas. We then folded these data into a Human PeptideAtlas 2012 build and mapped it to Swiss-Prot, a protein sequence database curated to contain one entry per human protein coding gene. We find that this latest PeptideAtlas build includes at least one peptide for each of ~12500 Swiss-Prot entries, leaving ~7500 gene products yet to be confidently cataloged. We characterize these "PA-unseen" proteins in terms of tissue localization, transcript abundance, and Gene Ontology enrichment, and propose reasons for their absence from PeptideAtlas and strategies for detecting them in the future.
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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.