Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Jan 4;12(1):162-71.
doi: 10.1021/pr301012j. Epub 2012 Dec 5.

The state of the human proteome in 2012 as viewed through PeptideAtlas

Terry Farrah  1 , Eric W Deutsch, Michael R Hoopmann, Janice L Hallows, Zhi Sun, Chung-Ying Huang, Robert L Moritz
Affiliations

The state of the human proteome in 2012 as viewed through PeptideAtlas

Terry Farrah et al. J Proteome Res. .

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.

PubMed Disclaimer

Conflict of interest statement

Conflict of interest disclosure

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
GO Cellular Component terms highly enriched among PA-unseen proteins. Terms with enrichment at P-value <= 10−10 are shaded, and only the nodes and edges which connect each of these terms with the root of the tree are depicted.
Figure 2
Figure 2
Microarray transcript analysis for proteins seen and unseen in PeptideAtlas. It is seen that PA-seen proteins tend to fall into the higher mean intensity bins (A) and have, on average, 2.5 times the mean intensity across all tissues (B, line 5). The microarray contained more probes for genes for PA-seen proteins than for PA-unseen because the array was biased toward proteins of high general interest (B, line 4). See text for details.
See this image and copyright information in PMC

References

    1. Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F, Zhang F, Zhang Y, Snyder M, Cheng Y, Chen R, Marko-Varga G, Deutsch EW, Kim H, Kwon JY, Aebersold R, Bairoch A, Taylor AD, Kim KY, Lee EY, Hochstrasser D, Legrain P, Hancock WS. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol. 2012;30(3):221–3. - PubMed
    1. Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers CH, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, Marko-Varga G, Salekdeh GH, Sechi S, Snyder M, Srivastava S, Uhlen M, Wu CH, Yamamoto T, Paik YK, Omenn GS. The human proteome project: current state and future direction. Mol Cell Proteomics. 2011;10(7):M111 009993. - PMC - PubMed
    1. Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R. The PeptideAtlas project. Nucleic Acids Res. 2006;34(Database issue):D655–8. - PMC - PubMed
    1. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kahari AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernandez-Suarez XM, Harrow J, Herrero J, Hubbard TJ, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SM. Ensembl 2012. Nucleic Acids Res. 2012;40(Database issue):D84–90. - PMC - PubMed
    1. Munoz J, Low TY, Kok YJ, Chin A, Frese CK, Ding V, Choo A, Heck AJ. The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Mol Syst Biol. 2011;7:550. - PMC - PubMed

Publication types