title: Strategy for degradomic-peptidomic analysis of human blood plasma.
abstract: Herein we describe a strategy for degradomic-peptidomic analyses. The human blood peptidome was isolated through application of AC/SEC, which enriched its components by >300-fold. The isolated peptidome components were separated by long column HRLC providing a peak capacity of approximately 300 for species having MWs of up to 20 kDa. The separated species were identified by the FT MS/MS-UStags sequencing method. We identified >200 peptidome components that originated from 29 protein substrates from the blood plasma of a single healthy person. The peptidome peptides identified had MWs range of 0.5-14 kDa and identifications were achieved with extremely low (near zero) false discovery rates through searching the IPI human protein database (approximately 70,000 entries). Some of the peptidome peptides identified have mutations and modifications such as acetylation, acetylhexosamine, amidation, cysteinylation, didehydro, oxidation, and pyro-glu. The capabilities described enable the global analysis of the peptidome peptides to identify degradome targets such as degradome proteases, proteases inhibitors, and other relevant substrates, the cleavage specificities for the degradation of individual substrates, as well as a potential basis for using the various extents of substrate degradation for diagnostic purposes.
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA. Yufeng.shen@pnl.gov
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Shen
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Nikola
authors.initials: N
authors.lastname: Tolić
authors.forename: Brianne O
authors.initials: BO
authors.lastname: Petritis
authors.forename: Rui
authors.initials: R
authors.lastname: Zhao
authors.forename: Ronald J
authors.initials: RJ
authors.lastname: Moore
authors.forename: Samuel O
authors.initials: SO
authors.lastname: Purvine
authors.forename: David G
authors.initials: DG
authors.lastname: Camp
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
mesh_terms: D000595:Amino Acid Sequence; D001774:Blood Chemical Analysis / Q000379:methods*; D001798:Blood Proteins / Q000737:chemistry* / Q000378:metabolism; D002846:Chromatography, Affinity; D002850:Chromatography, Gel; D006801:Humans; D008969:Molecular Sequence Data; D008970:Molecular Weight; D009154:Mutation; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry
chemical_list: D001798:Blood Proteins; D010446:Peptide Fragments