Isoform analysis of LC-MS/MS data from multidimensional fractionation of the serum proteome.
We developed a visualization approach for the identification of protein isoforms, precursor/mature protein combinations, and fragments from LC-MS/MS analysis of multidimensional fractionation of serum and plasma proteins. We also describe a pattern recognition algorithm to automatically detect and flag potentially heterogeneous species of proteins in proteomic experiments that involve extensive fractionation and result in a large number of identified serum or plasma proteins in an experiment. Examples are given of proteins with known isoforms that validate our approach and present a subset of precursor/mature protein pairs that were detected with this approach. Potential applications include identification of differentially expressed isoforms in disease states.
Krasnoselsky
Alexei L
AL
Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. akrasnos@fhcrc.org
Faca
Vitor M
VM
Pitteri
Sharon J
SJ
Zhang
Qing
Q
Hanash
Samir M
SM
D000465:Algorithms; D001798:Blood Proteins / Q000032:analysis* / Q000737:chemistry / Q000302:isolation & purification; D002135:Calcium-Binding Proteins / Q000032:analysis / Q000737:chemistry; D002851:Chromatography, High Pressure Liquid; D002852:Chromatography, Ion Exchange; D002853:Chromatography, Liquid / Q000379:methods*; D006801:Humans; D010363:Pattern Recognition, Automated; D010446:Peptide Fragments / Q000032:analysis / Q000737:chemistry; D007862:Phosphatidylcholine-Sterol O-Acyltransferase / Q000032:analysis / Q000737:chemistry; D020033:Protein Isoforms / Q000032:analysis / Q000737:chemistry / Q000302:isolation & purification; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods; D011516:Prothrombin / Q000032:analysis / Q000737:chemistry; D012697:Serine Endopeptidases / Q000032:analysis / Q000737:chemistry; D053719:Tandem Mass Spectrometry / Q000379:methods*; D014357:Trypsin / Q000737:chemistry
D001798:Blood Proteins; D002135:Calcium-Binding Proteins; D010446:Peptide Fragments; D020033:Protein Isoforms; D020543:Proteome; C060820:fibulin; D011516:Prothrombin; D007862:Phosphatidylcholine-Sterol O-Acyltransferase; C081092:HGF activator; D012697:Serine Endopeptidases; D014357:Trypsin