title: Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project.
abstract: 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.
authors.affiliation: University of Michigan, Ann Arbor, MI 48109-2218, USA.
authors.forename: Marcin
authors.initials: M
authors.lastname: Adamski
authors.forename: Thomas
authors.initials: T
authors.lastname: Blackwell
authors.forename: Rajasree
authors.initials: R
authors.lastname: Menon
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Chris
authors.initials: C
authors.lastname: Taylor
authors.forename: Gilbert S
authors.initials: GS
authors.lastname: Omenn
authors.forename: David J
authors.initials: DJ
authors.lastname: States
mesh_terms: 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
chemical_list: D001798:Blood Proteins; D010455:Peptides; D020543:Proteome