A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas

Terry Farrah, Eric W. Deutsch, Gilbert S. Omenn, David S. Campbell, Zhi Sun, Julie A. Bletz, Parag Mallick, Jonathan E. Katz, Johan Malmström, Reto Ossola, Julian D. Watts, Biaoyang Lin, Hui Zhang, Robert L. Moritz, Ruedi Aebersold

Research output: Contribution to journalArticle

Abstract

Human blood plasma can be obtained relatively noninvasively and contains proteins from most, if not all, tissues of the body. Therefore, an extensive, quantitative catalog of plasma proteins is an important starting point for the discovery of disease biomarkers. In 2005, we showed that different proteomics measurements using different sample preparation and analysis techniques identify significantly different sets of proteins, and that a comprehensive plasma proteome can be compiled only by combining data from many different experiments. Applying advanced computational methods developed for the analysis and integration of very large and diverse data sets generated by tandem MS measurements of tryptic peptides, we have now compiled a high-confidence human plasma proteome reference set with well over twice the identified proteins of previous high-confidence sets. It includes a hierarchy of protein identifications at different levels of redundancy following a clearly defined scheme, which we propose as a standard that can be applied to any proteomics data set to facilitate cross-proteome analyses. Further, to aid in development of blood-based diagnostics using techniques such as selected reaction monitoring, we provide a rough estimate of protein concentrations using spectral counting. We identified 20,433 distinct peptides, from which we inferred a highly nonredundant set of 1929 protein sequences at a false discovery rate of 1%. We have made this resource available via PeptideAtlas, a large, multiorganism, publicly accessible compendium of peptides identified in tandem MS experiments conductedby laboratories around the world.

Original languageEnglish (US)
JournalMolecular and Cellular Proteomics
Volume10
Issue number9
DOIs
StatePublished - Sep 2011

Fingerprint

Plasma (human)
Proteome
Proteins
Proteomics
Peptides
Blood
Plasmas
Biomarkers
Computational methods
Redundancy
Blood Proteins
Experiments
Tissue
Monitoring

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Analytical Chemistry

Cite this

Farrah, T., Deutsch, E. W., Omenn, G. S., Campbell, D. S., Sun, Z., Bletz, J. A., ... Aebersold, R. (2011). A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Molecular and Cellular Proteomics, 10(9). https://doi.org/10.1074/mcp.M110.006353

A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. / Farrah, Terry; Deutsch, Eric W.; Omenn, Gilbert S.; Campbell, David S.; Sun, Zhi; Bletz, Julie A.; Mallick, Parag; Katz, Jonathan E.; Malmström, Johan; Ossola, Reto; Watts, Julian D.; Lin, Biaoyang; Zhang, Hui; Moritz, Robert L.; Aebersold, Ruedi.

In: Molecular and Cellular Proteomics, Vol. 10, No. 9, 09.2011.

Research output: Contribution to journalArticle

Farrah, T, Deutsch, EW, Omenn, GS, Campbell, DS, Sun, Z, Bletz, JA, Mallick, P, Katz, JE, Malmström, J, Ossola, R, Watts, JD, Lin, B, Zhang, H, Moritz, RL & Aebersold, R 2011, 'A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas', Molecular and Cellular Proteomics, vol. 10, no. 9. https://doi.org/10.1074/mcp.M110.006353
Farrah, Terry ; Deutsch, Eric W. ; Omenn, Gilbert S. ; Campbell, David S. ; Sun, Zhi ; Bletz, Julie A. ; Mallick, Parag ; Katz, Jonathan E. ; Malmström, Johan ; Ossola, Reto ; Watts, Julian D. ; Lin, Biaoyang ; Zhang, Hui ; Moritz, Robert L. ; Aebersold, Ruedi. / A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. In: Molecular and Cellular Proteomics. 2011 ; Vol. 10, No. 9.
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