title: Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.
abstract: Protein phosphorylation is essential for numerous cellular processes. Large-scale profiling of phosphoproteins continues to enhance the depth and speed at which we understand these processes. The development of effective phosphoprotein and peptide enrichment techniques and improvements to mass spectrometric instrumentation have intensified phosphoproteomic research in recent years, leading to unprecedented achievements. Here, we describe a large-scale phosphorylation analysis of alpha-factor-arrested yeast. Using a multidimensional separation strategy involving preparative SDS-PAGE for prefractionation, in-gel digestion with trypsin, and immobilized metal affinity chromatography (IMAC) enrichment of phosphopeptides, followed by LC-MS/MS analysis employing a hybrid LTQ-Orbitrap mass spectrometer, we were able to catalog a substantial portion of the phosphoproteins present in yeast whole-cell lysate. This analysis yielded the confident identification of 2288 nonredundant phosphorylation sites from 985 proteins. The ambiguity score (Ascore) algorithm was utilized to determine the certainty of site localization for the entire data set. In addition, the size of the data set permitted extraction of known and novel kinase motifs using the Motif-X algorithm. Finally, a large number of members of the pheromone signaling pathway were found as phosphoproteins and are discussed.
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Xue
authors.initials: X
authors.lastname: Li
authors.forename: Scott A
authors.initials: SA
authors.lastname: Gerber
authors.forename: Adam D
authors.initials: AD
authors.lastname: Rudner
authors.forename: Sean A
authors.initials: SA
authors.lastname: Beausoleil
authors.forename: Wilhelm
authors.initials: W
authors.lastname: Haas
authors.forename: Judit
authors.initials: J
authors.lastname: Villén
authors.forename: Joshua E
authors.initials: JE
authors.lastname: Elias
authors.forename: Steve P
authors.initials: SP
authors.lastname: Gygi
mesh_terms: D002845:Chromatography; D004591:Electrophoresis, Polyacrylamide Gel; D010675:Pheromones; D010748:Phosphopeptides / Q000032:analysis; D010750:Phosphoproteins / Q000032:analysis*; D010766:Phosphorylation; D040901:Proteomics / Q000379:methods*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis*; D015398:Signal Transduction; D053719:Tandem Mass Spectrometry; D014357:Trypsin / Q000378:metabolism
chemical_list: D010675:Pheromones; D010748:Phosphopeptides; D010750:Phosphoproteins; D029701:Saccharomyces cerevisiae Proteins; D014357:Trypsin