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Software for analysing ion mobility mass spectrometry data to improve peptide identification
Author(s) -
Xia Dong,
Ghali Fawaz,
Gaskell Simon J.,
O'Cualain Ronan,
Sims Paul F. G.,
Jones Andrew R.
Publication year - 2012
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201200029
Subject(s) - ion mobility spectrometry , software , fragmentation (computing) , computer science , mass spectrometry , proteomics , identification (biology) , ion , peptide , chemistry , data mining , chromatography , programming language , biology , biochemistry , botany , organic chemistry , gene
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/.