Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project

Omenn, Gilbert S.; Lane, Lydie; Overall, Christopher M.; Corrales, Fernando J.; Schwenk, Jochen M.; Paik, Young‐Ki; Eyk, Jennifer E. Van; Liu, Siqi; Pennington, Stephen R.; Snyder, M; Baker, Mark S.; Deutsch, Eric W.

doi:10.1021/acs.jproteome.9b00434

Cited by 44 publications

(65 citation statements)

References 84 publications

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“…It contributes to the HUPO human antibody initiative. The current release contains data based on 26,371 well-characterised antibodies targeting 17,058 unique proteins (86% of the human proteome based on the current metrics [6]. Currently divided into three different sub-atlases (the Tissue Atlas [7], the Pathology Atlas [8] and the Cell Atlas [9]) it covers a wide spectrum of spatial localization at different levels, as well as addressing the consequence of human genes on patient survival.…”

Section: Session C Antibody and Biosensor-based Applications For Promentioning

confidence: 99%

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The omics revolution: beyond genomics. A meeting report

Nice

2020

Clin Proteom

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The "omics revolution: beyond genomics" satellite meeting, run under the auspices of the Australian Peptide Association, The Human Proteome Organisation (HUPO) and the HUPO Australia/New Zealand Chromosome 7 initiative, was held at the Oaks Resort, Port Douglas, Queensland, Australia, on 8th September 2019, immediately prior to the 13th Australian Peptide Conference. The meeting, which had over 100 participants representing Australasia, Europe and America, focused on recent advances in omics-related technologies, including mass spectrometry, biosensors and CryoEM, which will assist in the clinical translation of proteomics towards precision/personalized medicine. An overview of the conference and a summary of the oral presentations are presented.

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Section: Session C Antibody and Biosensor-based Applications For Promentioning

confidence: 99%

“…This year there were over 100 delegates from 16 countries with almost half coming from overseas. This included strong representation from China (16), Japan (7), USA (6), and Singapore (5). Delegates represented academia, biotechnology, the pharmaceutical industry and the legal and patent fraternity.…”

Section: Introductionmentioning

confidence: 99%

The omics revolution: beyond genomics. A meeting report

Nice

2020

Clin Proteom

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“…Our understanding of the human proteome continues to evolve rapidly and the use of older versions may lead to confusion and outdated claims. Generally, neXtProt curators update regularly, with their prior January release relied upon for HPP Journal of Proteome Research Special Issue data analysis/reanalysis and which effectively is reflected as the annual HPP metrics 3,6,[9][10][11]20 . Guideline 4 merges all previous FDR-related guidelines (4 -9 in version 2.1) into a single top-level entry with four subitems designed to streamline this section.…”

Section: Sectionmentioning

confidence: 99%

“…The Human Proteome Organization's 1 (HUPO) Human Proteome Project 2,3 (HPP) was launched in 2010 as an international endeavor to build on the success of the Human Genome Project 4,5 by characterizing the products of the ~20,000 human protein-coding genes. As of January 2019, 17,694 proteins demonstrated compelling mass spectrometry (MS) or non-MS protein-level evidence in neXtProt (i.e., PE1), leaving 2129 proteins without strong evidence (PE2, 3,4) that were have been designated as the HPP's 'missing proteins' 6 . The PE2,3,4 missing proteins represented 10.7% of all neXtProt's PE2,3,4 proteins.…”

Section: Introductionmentioning

confidence: 99%

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

Deutsch

Lane

Overall

et al. 2019

Preprint

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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 falsepositive 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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“…The 2020-01-17 release contains 20,350 entries, of which 1,899 (9%) are 'missing proteins' (PE2-4) awaiting experimental validation. Over the last 5 years this proportion has steadily decreased thanks to the global efforts of the community to profile human samples with mass spectrometers having increasing precision and sensitivity, and we can reasonably expect that it will continue to do so [4]. Among the validated proteins (PE1), 1,254 are devoid of functional annotation, either predicted or experimental.…”

Section: Introductionmentioning

confidence: 99%