Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project.
The pilot phase of the HUPO Plasma Proteome Project (PPP) is an international collaboration to catalog the protein composition of human blood plasma and serum by analyzing standardized aliquots of reference serum and plasma specimens using a variety of experimental techniques. Data management for this project included collection, integration, analysis, and dissemination of findings from participating organizations world-wide. Accomplishing this task required a communication and coordination infrastructure specific enough to support meaningful integration of results from all participants, but flexible enough to react to changing requirements and new insights gained during the course of the project and to allow participants with varying informatics capabilities to contribute. Challenges included integrating heterogeneous data, reducing redundant information to minimal identification sets, and data annotation. Our data integration workflow assembles a minimal and representative set of protein identifications, which account for the contributed data. It accommodates incomplete concordance of results from different laboratories, ambiguity and redundancy in contributed identifications, and redundancy in the protein sequence databases. Recommendations of the PPP for future large-scale proteomics endeavors are described.
Adamski
Marcin
M
University of Michigan, Ann Arbor, MI 48109-2218, USA.
Blackwell
Thomas
T
Menon
Rajasree
R
Martens
Lennart
L
Hermjakob
Henning
H
Taylor
Chris
C
Omenn
Gilbert S
GS
States
David J
DJ
D000465:Algorithms; D001798:Blood Proteins / Q000737:chemistry*; D030562:Databases, Protein; D005189:False Positive Reactions; D006801:Humans; D007391:International Cooperation; D015233:Models, Statistical; D010455:Peptides / Q000737:chemistry; D010865:Pilot Projects; D016012:Poisson Distribution; D020543:Proteome / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012016:Reference Values; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
D001798:Blood Proteins; D010455:Peptides; D020543:Proteome