title: A functional annotation of subproteomes in human plasma.
abstract: 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 intra-membrane 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.
authors.affiliation: Department of Physiology and Medicine, Division of Cardiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA.
authors.forename: Peipei
authors.initials: P
authors.lastname: Ping
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Vondriska
authors.forename: Chad J
authors.initials: CJ
authors.lastname: Creighton
authors.forename: T K B
authors.initials: TK
authors.lastname: Gandhi
authors.forename: Ziping
authors.initials: Z
authors.lastname: Yang
authors.forename: Rajasree
authors.initials: R
authors.lastname: Menon
authors.forename: Min-Seok
authors.initials: MS
authors.lastname: Kwon
authors.forename: Sang Yun
authors.initials: SY
authors.lastname: Cho
authors.forename: Garry
authors.initials: G
authors.lastname: Drwal
authors.forename: Markus
authors.initials: M
authors.lastname: Kellmann
authors.forename: Suraj
authors.initials: S
authors.lastname: Peri
authors.forename: Shubha
authors.initials: S
authors.lastname: Suresh
authors.forename: Mads
authors.initials: M
authors.lastname: Gronborg
authors.forename: Henrik
authors.initials: H
authors.lastname: Molina
authors.forename: Raghothama
authors.initials: R
authors.lastname: Chaerkady
authors.forename: B
authors.initials: B
authors.lastname: Rekha
authors.forename: Arun S
authors.initials: AS
authors.lastname: Shet
authors.forename: Robert E
authors.initials: RE
authors.lastname: Gerszten
authors.forename: Haifeng
authors.initials: H
authors.lastname: Wu
authors.forename: Mark
authors.initials: M
authors.lastname: Raftery
authors.forename: Valerie
authors.initials: V
authors.lastname: Wasinger
authors.forename: Peter
authors.initials: P
authors.lastname: Schulz-Knappe
authors.forename: Samir M
authors.initials: SM
authors.lastname: Hanash
authors.forename: Young-Ki
authors.initials: YK
authors.lastname: Paik
authors.forename: William S
authors.initials: WS
authors.lastname: Hancock
authors.forename: David J
authors.initials: DJ
authors.lastname: States
authors.forename: Gilbert S
authors.initials: GS
authors.lastname: Omenn
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Pandey
mesh_terms: D001777:Blood Coagulation; D001798:Blood Proteins / Q000737:chemistry*; D002845:Chromatography; D019295:Computational Biology; D004247:DNA / Q000737:chemistry; D030562:Databases, Protein; D006801:Humans; D007249:Inflammation; D037102:Lectins / Q000737:chemistry; D008099:Liver / Q000378:metabolism; D013058:Mass Spectrometry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D010587:Phagocytosis; D011485:Protein Binding; D011499:Protein Processing, Post-Translational; D021382:Protein Sorting Signals; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D013223:Statistics as Topic; D014357:Trypsin / Q000494:pharmacology
chemical_list: D001798:Blood Proteins; D037102:Lectins; D010455:Peptides; D021382:Protein Sorting Signals; D020543:Proteome; D004247:DNA; D014357:Trypsin