ArticleJournal of proteome research2019
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0.
Article in Journal of proteome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers, 1 of them a synthesis that pooled it.
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Who cites it
66 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Ethical Principles, Constraints and Opportunities in Clinical Proteomics.Molecular & cellular proteomics : MCP · 2021Pooled it
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- High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.bioRxiv : the preprint server for biology · 2025Article
- Proteogenomics-enabled discovery of novel small open reading frame (sORF)-encoded polypeptides in human and mouse tissues.Nucleic acids research · 2025Article
- Evaluation of PE5 Entries on the Human Proteome Project Target List.Journal of proteome research · 2025Article
- From Cell Lines to Patients: Dissecting the Proteomic Landscape of Exosomes in Breast Cancer.Diagnostics (Basel, Switzerland) · 2025Article
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- Quetzal: Comprehensive Peptide Fragmentation Annotation and Visualization.Journal of proteome research · 2025Article
- Chronic CRYPTOCHROME deficiency enhances cell-intrinsic antiviral defences.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Storage conditions differentially alter the human tooth enamel proteome.Frontiers in dental medicine · 2025Article
- Integrating proteomics and machine learning reveals characteristics and risks of lymph node-independent distant metastasis in colorectal cancer.Frontiers in immunology · 2025Article
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- The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends.Journal of proteome research · 2024Article
- Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature.Journal of proteome research · 2024Review
- The 2024 Report on the Human Proteome from the HUPO Human Proteome Project.Journal of proteome research · 2024Review
- Proteomic Profiling of Pre- and Post-Surgery Saliva of Glioblastoma Patients: A Pilot Investigation.International journal of molecular sciences · 2024Article
- PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.Computational and structural biotechnology journal · 2024Article
6 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
14 authors.
Funding
Abstract
The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems, and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well, and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ∼20 000 human proteins encoded by the human genome.
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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.