title: A global analysis of peptide fragmentation variability.
abstract: Understanding the fragmentation process in MS/MS experiments is vital when trying to validate the results of such experiments, and one way of improving our understanding is to analyze existing data. We here present our findings from an analysis of a large and diverse data set of MS/MS-based peptide identifications, in which each peptide has been identified from multiple spectra, recorded on two commonly used types of electrospray instruments. By analyzing these data we were able to study fragmentation variability on three levels: (i) variation in detection rates and intensities for fragment ions from the same peptide sequence measured multiple times on a single instrument; (ii) consistency of rank-based fragmentation patterns; and (iii) a set of general observations on fragment ion occurrence in MS/MS experiments, regardless of sequence. Our results confirm that substantial variation can be found at all levels, even when high-quality identifications are used and the experimental conditions as well as the peptide sequences are kept constant. Finally, we discuss the observed variability in light of ongoing efforts to create spectral libraries and predictive software for target selection in targeted proteomics.
authors.affiliation: Department of Informatics, University of Bergen, Bergen, Norway.
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
authors.forename: Ingvar
authors.initials: I
authors.lastname: Eidhammer
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D000595:Amino Acid Sequence; D000704:Analysis of Variance; D003627:Data Interpretation, Statistical; D030562:Databases, Protein / Q000706:statistics & numerical data; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry / Q000302:isolation & purification*; D019151:Peptide Library; D040901:Proteomics / Q000706:statistics & numerical data*; D012984:Software; D021241:Spectrometry, Mass, Electrospray Ionization / Q000706:statistics & numerical data; D053719:Tandem Mass Spectrometry / Q000706:statistics & numerical data*
chemical_list: D010446:Peptide Fragments; D019151:Peptide Library