title: An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics.
abstract: Currently, the precursor ion selection strategies in LC-MS mainly choose the most prominent peptide signals for MS/MS analysis. Consequently, high-abundance proteins are identified by MS/MS of many peptides, whereas proteins of lower abundance might elude identification. We present a novel, iterative and result-driven approach for precursor ion selection that significantly increases the efficiency of an MS/MS analysis by decreasing data redundancy and analysis time. By simulating different strategies for precursor ion selection on an existing data set, we compare our method to existing result-driven strategies and evaluate its performance with regard to mass accuracy, database size, and sample complexity.
authors.affiliation: Max Planck Institute for Molecular Genetics, Department Vertebrate Genomics, Ihnestr. 63-73, D-14195 Berlin, Germany. zerck@molgen.mpg.de
authors.forename: Alexandra
authors.initials: A
authors.lastname: Zerck
authors.forename: Eckhard
authors.initials: E
authors.lastname: Nordhoff
authors.forename: Anja
authors.initials: A
authors.lastname: Resemann
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Mirgorodskaya
authors.forename: Detlef
authors.initials: D
authors.lastname: Suckau
authors.forename: Knut
authors.initials: K
authors.lastname: Reinert
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.forename: Johan
authors.initials: J
authors.lastname: Gobom
mesh_terms: D000465:Algorithms; D002460:Cell Line; D002853:Chromatography, Liquid / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism; D006801:Humans; D007477:Ions; D013058:Mass Spectrometry / Q000379:methods*; D015233:Models, Statistical; D010455:Peptides / Q000032:analysis; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D007477:Ions; D010455:Peptides; D011506:Proteins