A functional annotation of subproteomes in human plasma

Peipei Ping, Thomas M. Vondriska, Chad J. Creighton, T. K.B. Gandhi, Ziping Yang, Rajasree Menon, Min Seok Kwon, Sang Yun Cho, Garry Drwal, Markus Kellmann, Suraj Peri, Shubha Suresh, Mads Gronborg, Henrik Molina, Raghothama Chaerkady, B. Rekha, Arun S. Shet, Robert E. Gerszten, Haifeng Wu, Mark RafteryValerie Wasinger, Peter Schulz-Knappe, Samir M. Hanash, Young Ki Paik, William S. Hancock, David J. States, Gilbert S. Omenn, Akhilesh Pandey

Research output: Contribution to journalArticlepeer-review

69 Scopus citations


The data collected by Human Proteome Organization's Plasma Proteome Pilot project phase was analyzed by members of our working group. Accordingly, a functional annotation of the human plasma proteome was carried out. Here, we report the findings of our analyses. First, bioinformatic analyses were undertaken to determine the likely sources of plasma proteins and to develop a protein interaction network of proteins identified in this project. Second, annotation of these proteins was performed in the context of functional subproteomes involved in the coagulation pathway, the mononuclear phagocytic system, the inflammation pathway, the cardiovascular system, and the liver; as well as the subset of proteins associated with DNA binding activities. Our analyses contributed to the Plasma Proteome Database (http://www. plasmaproteomedatabase.org), an annotated database of plasma proteins identified by HPPP as well as from other published studies. In addition, we address several methodological considerations including the selective enrichment of post-translationally modified proteins by the use of multi-lectin chromatography as well as the use of peptidomic techniques to characterize the low molecular weight proteins in plasma. Furthermore, we have performed additional analyses of peptide identification data to annotate cleavage of signal peptides, sites of intramembrane proteolysis and post-translational modifications. The HPPP-organized, multi-laboratory effort, as described herein, resulted in much synergy and was essential to the success of this project.

Original languageEnglish (US)
Pages (from-to)3506-3519
Number of pages14
Issue number13
StatePublished - Aug 2005


  • Annotation
  • Bioinformatics
  • MS
  • Proteomics
  • Serum

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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