title: A multidimensional chromatography technology for in-depth phosphoproteome analysis.
abstract: Protein phosphorylation is a post-translational modification widely used to regulate cellular responses. Recent studies showed that global phosphorylation analysis could be used to study signaling pathways and to identify targets of protein kinases in cells. A key objective of global phosphorylation analysis is to obtain an in-depth mapping of low abundance protein phosphorylation in cells; this necessitates the use of suitable separation techniques because of the complexity of the phosphoproteome. Here we developed a multidimensional chromatography technology, combining IMAC, hydrophilic interaction chromatography, and reverse phase LC, for phosphopeptide purification and fractionation. Its application to the yeast Saccharomyces cerevisiae after DNA damage led to the identification of 8764 unique phosphopeptides from 2278 phosphoproteins using tandem MS. Analysis of two low abundance proteins, Rad9 and Mrc1, revealed that approximately 50% of their phosphorylation was identified via this global phosphorylation analysis. Thus, this technology is suited for in-depth phosphoproteome studies.
authors.affiliation: Ludwig Institute for Cancer Research, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.
authors.forename: Claudio P
authors.initials: CP
authors.lastname: Albuquerque
authors.forename: Marcus B
authors.initials: MB
authors.lastname: Smolka
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Payne
authors.forename: Vineet
authors.initials: V
authors.lastname: Bafna
authors.forename: Jimmy
authors.initials: J
authors.lastname: Eng
authors.forename: Huilin
authors.initials: H
authors.lastname: Zhou
mesh_terms: D002845:Chromatography / Q000379:methods; D016000:Cluster Analysis; D004249:DNA Damage / Q000502:physiology; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D010748:Phosphopeptides / Q000032:analysis / Q000378:metabolism; D010750:Phosphoproteins / Q000032:analysis* / Q000378:metabolism; D011485:Protein Binding; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics
chemical_list: D010748:Phosphopeptides; D010750:Phosphoproteins; D020543:Proteome