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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including

Gilbert S Omenn1, Lydie Lane2, Emma K Lundberg3

  • 1Department of Computational Medicine and Bioinformatics, University of Michigan , 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States.

Journal of Proteome Research
|August 4, 2016
PubMed
Summary
This summary is machine-generated.

The Human Proteome Project (HPP) advances human proteome completion by identifying proteins and their variations. New guidelines ensure higher confidence in protein identifications, enhancing proteomics integration with genomics.

Keywords:
GPMDBHuman Protein AtlasN-terminiPTMs (post-translational modifications)PeptideAtlasSAAV (single amino acid variants)guidelinesmetricsneXtProtsplice isoforms

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Area of Science:

  • Proteomics and Genomics
  • Biomedical Research
  • Human Proteome Characterization

Background:

  • The Human Proteome Project (HPP) aims to complete the human proteome's protein parts list.
  • It seeks to integrate proteomics as a counterpart to genomics in life sciences.
  • Previous efforts established a baseline, but with less stringent identification criteria.

Purpose of the Study:

  • To report on the progress of the HPP, focusing on the completion of the human proteome.
  • To detail the application of updated HPP Guidelines for Mass Spectrometry Data Interpretation (v2.1).
  • To highlight advancements in identifying protein sequence variants, PTMs, and splice isoforms.

Main Methods:

  • Reanalysis of human mass spectrometry datasets using standardized protocols (PeptideAtlas, GPMDB).
  • Curation and integration of data in neXtProt for an authoritative human proteome compendium.
  • Application of stringent quality filters and updated guidelines (v2.1) requiring two unique proteotypic peptides.

Main Results:

  • The Human Proteome in neXtProt (v2016-02) now includes 16,518 confident protein identifications (PE Level 1).
  • Updated guidelines (v2.0) led to 485 proteins previously considered PE1 now having insufficient evidence, reducing false positives.
  • Databases like PeptideAtlas, GPMDB, and neXtProt provide rich information on PTMs, SAAVs, and splice isoforms.

Conclusions:

  • The HPP has significantly increased confident protein identifications through standardized analysis and stringent guidelines.
  • The project is making strides in characterizing protein variants and isoforms, crucial for understanding human biology and disease.
  • Proteomics resources like neXtProt, PeptideAtlas, and GPMDB are essential for advancing proteome research and its integration with genomics.