A functional annotation of subproteomes in human plasma.
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.
Ping
Peipei
P
Department of Physiology and Medicine, Division of Cardiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA.
Vondriska
Thomas M
TM
Creighton
Chad J
CJ
Gandhi
T K B
TK
Yang
Ziping
Z
Menon
Rajasree
R
Kwon
Min-Seok
MS
Cho
Sang Yun
SY
Drwal
Garry
G
Kellmann
Markus
M
Peri
Suraj
S
Suresh
Shubha
S
Gronborg
Mads
M
Molina
Henrik
H
Chaerkady
Raghothama
R
Rekha
B
B
Shet
Arun S
AS
Gerszten
Robert E
RE
Wu
Haifeng
H
Raftery
Mark
M
Wasinger
Valerie
V
Schulz-Knappe
Peter
P
Hanash
Samir M
SM
Paik
Young-Ki
YK
Hancock
William S
WS
States
David J
DJ
Omenn
Gilbert S
GS
Pandey
Akhilesh
A
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
D001798:Blood Proteins; D037102:Lectins; D010455:Peptides; D021382:Protein Sorting Signals; D020543:Proteome; D004247:DNA; D014357:Trypsin