title: Software for analysing ion mobility mass spectrometry data to improve peptide identification.
abstract: The development of ion mobility (IM) MS instruments has the capability to provide an added dimension to peptide analysis pipelines in proteomics, but, as yet, there are few software tools available for analysing such data. IM can be used to provide additional separation of parent ions or product ions following fragmentation. In this work, we have created a set of software tools that are capable of converting three dimensional IM data generated from analysis of fragment ions into a variety of formats used in proteomics. We demonstrate that IM can be used to calculate the charge state of a fragment ion, demonstrating the potential to improve peptide identification by excluding non-informative ions from a database search. We also provide preliminary evidence of structural differences between b and y ions for certain peptide sequences but not others. All software tools and data sets are made available in the public domain at http://code.google.com/p/ion-mobility-ms-tools/.
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
authors.forename: Dong
authors.initials: D
authors.lastname: Xia
authors.forename: Fawaz
authors.initials: F
authors.lastname: Ghali
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Gaskell
authors.forename: Ronan
authors.initials: R
authors.lastname: O'Cualain
authors.forename: Paul F G
authors.initials: PF
authors.lastname: Sims
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jones
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D016014:Linear Models; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis / Q000737:chemistry*; D012984:Software
chemical_list: D010455:Peptides