title: An automated method for scanning LC-MS data sets for significant peptides and proteins, including quantitative profiling and interactive confirmation.
abstract: Differential quantification of proteins and peptides by LC-MS is a promising method to acquire knowledge about biological processes, and for finding drug targets and biomarkers. However, differential protein analysis using LC-MS has been held back by the lack of suitable software tools. Large amounts of experimental data are easily generated in protein and peptide profiling experiments, but data analysis is time-consuming and labor-intensive. Here, we present a fully automated method for scanning LC-MS/MS data for biologically significant peptides and proteins, including support for interactive confirmation and further profiling. By studying peptide mixtures of known composition, we demonstrate that peptides present in different amounts in different groups of samples can be automatically screened for using statistical tests. A linear response can be obtained over almost 3 orders of magnitude, facilitating further profiling of peptides and proteins of interest. Furthermore, we apply the method to study the changes of endogenous peptide levels in mouse brain striatum after administration of reserpine, a classical model drug for inducing Parkinson disease symptoms.
authors.affiliation: GE Healthcare Bio-Sciences AB, SE-75184, Uppsala, Sweden.
authors.forename: Anders
authors.initials: A
authors.lastname: Kaplan
authors.forename: Malin
authors.initials: M
authors.lastname: Söderström
authors.forename: David
authors.initials: D
authors.lastname: Fenyö
authors.forename: Anna
authors.initials: A
authors.lastname: Nilsson
authors.forename: Maria
authors.initials: M
authors.lastname: Fälth
authors.forename: Karl
authors.initials: K
authors.lastname: Sköld
authors.forename: Marcus
authors.initials: M
authors.lastname: Svensson
authors.forename: Harald
authors.initials: H
authors.lastname: Pettersen
authors.forename: Staffan
authors.initials: S
authors.lastname: Lindqvist
authors.forename: Per
authors.initials: P
authors.lastname: Svenningsson
authors.forename: Per E
authors.initials: PE
authors.lastname: Andrén
authors.forename: Lennart
authors.initials: L
authors.lastname: Björkesten
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002853:Chromatography, Liquid; D003342:Corpus Striatum / Q000737:chemistry; D013058:Mass Spectrometry; D051379:Mice; D008969:Molecular Sequence Data; D010300:Parkinson Disease / Q000378:metabolism; D010455:Peptides / Q000032:analysis*; D011506:Proteins / Q000032:analysis*; D012984:Software
chemical_list: D010455:Peptides; D011506:Proteins