The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.

Schwenk JM; Omenn GS; Sun Z; Campbell DS; Baker MS; Overall CM; Aebersold R; Moritz RL; Deutsch EW

doi:10.1021/acs.jproteome.7b00467

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The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.

Schwenk JM Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology , Tomtebodavägen 23, SE-171 65 Solna, Sweden.
Omenn GS Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan , Ann Arbor, Michigan 48109-2218, United States.
Sun Z Institute for Systems Biology , Seattle, Washington 98109, United States.
Campbell DS Institute for Systems Biology , Seattle, Washington 98109, United States.
Baker MS Department of Biomedical Sciences, Faculty of Medicine and Health Science, Macquarie University , Sydney, New South Wales 2109, Australia.
Overall CM Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia , Vancouver, Canada.
Aebersold R Department of Biology, Institute of Molecular Systems Biology, ETH Zurich , Zurich, Switzerland.
Moritz RL Institute for Systems Biology , Seattle, Washington 98109, United States.
Deutsch EW Institute for Systems Biology , Seattle, Washington 98109, United States.

2017-09-23

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Journal of proteome research. - 2017

English Human blood plasma provides a highly accessible window to the proteome of any individual in health and disease. Since its inception in 2002, the Human Proteome Organization's Human Plasma Proteome Project (HPPP) has been promoting advances in the study and understanding of the full protein complement of human plasma and on determining the abundance and modifications of its components. In 2017, we review the history of the HPPP and the advances of human plasma proteomics in general, including several recent achievements. We then present the latest 2017-04 build of Human Plasma PeptideAtlas, which yields ∼43 million peptide-spectrum matches and 122,730 distinct peptide sequences from 178 individual experiments at a 1% protein-level FDR globally across all experiments. Applying the latest Human Proteome Project Data Interpretation Guidelines, we catalog 3509 proteins that have at least two non-nested uniquely mapping peptides of nine amino acids or more and >1300 additional proteins with ambiguous evidence. We apply the same two-peptide guideline to historical PeptideAtlas builds going back to 2006 and examine the progress made in the past ten years in plasma proteome coverage. We also compare the distribution of proteins in historical PeptideAtlas builds in various RNA abundance and cellular localization categories. We then discuss advances in plasma proteomics based on targeted mass spectrometry as well as affinity assays, which during early 2017 target ∼2000 proteins. Finally, we describe considerations about sample handling and study design, concluding with an outlook for future advances in deciphering the human plasma proteome.

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