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HUPO Plasma Proteome Project - Advancement of biomarker discovery and validation through the HUPO plasma proteome project

ABSTRACT: esi-quadrupole tof survey of tryptic peptides from HUPO pooled Human plasma or serum specimen: b1-serum.

INSTRUMENT(S): LCQ Deca, instrument model, LTQ, Waters instrument model, Q TRAP, 4700 Proteomics Analyzer, QSTAR

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma, Blood Serum

SUBMITTER: DAVE THORNEYCROFT

PROVIDER: PRD000002 | Pride | 2007-04-23

REPOSITORIES: Pride

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			Action	DRS
	PRIDE_Exp_Complete_Ac_10.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_10.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_11.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_11.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_12.pride.mztab.gz	Mztab

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International collaboration in clinical chemistry and laboratory medicine: the Human Proteome Organization (HUPO) Plasma Proteome Project.

Omenn Gilbert S GS

Clinical chemistry and laboratory medicine 20040101 1

PMID: 15061371

Publication: 1/9

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Project description:The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".

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Project description:The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17 008 confident protein identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 ( https://hupo.org/Guidelines ), up from 13 664 in 2012-12 and 16 518 in 2016-04. Remaining to be found by mass spectrometry and other methods are 2579 "missing proteins" (PE2+3+4), down from 2949 in 2016. PeptideAtlas 2017-01 has 15 173 canonical proteins, accounting for nearly all of the 15 290 PE1 proteins based on MS data. These resources have extensive data on PTMs, single amino acid variants, and splice isoforms. The Human Protein Atlas v16 has 10 492 highly curated protein entries with tissue and subcellular spatial localization of proteins and transcript expression. Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.

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