Technical Brief

Software for analysing ion mobility mass spectrometry data to improve peptide identification

  1. Dong Xia1,
  2. Fawaz Ghali1,
  3. Simon J. Gaskell2,
  4. Ronan O'Cualain3,
  5. Paul F. G. Sims3,
  6. Andrew R. Jones1,*

Article first published online: 28 JUN 2012

DOI: 10.1002/pmic.201200029

Issue

PROTEOMICS

PROTEOMICS

Volume 12, Issue 12, pages 1912–1916, June 2012

Additional Information

How to Cite

Xia, D., Ghali, F., Gaskell, S. J., O'Cualain, R., Sims, P. F. G. and Jones, A. R. (2012), Software for analysing ion mobility mass spectrometry data to improve peptide identification. Proteomics, 12: 1912–1916. doi: 10.1002/pmic.201200029

Author Information

  1. 1

    Institute of Integrative Biology, University of Liverpool, Liverpool, UK

  2. 2

    Queen Mary University of London, London, UK

  3. 3

    Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester, UK

*Correspondence: Dr. Andrew Robert Jones, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
E-mail:andrew.jones@liv.ac.uk
Fax: +44 151 795 4408

  1. Colour Online: See the article online to view Figs. 1 and 2 in colour.

Publication History

  1. Issue published online: 28 JUN 2012
  2. Article first published online: 28 JUN 2012
  3. Accepted manuscript online: 23 MAY 2012 07:56AM EST
  4. Manuscript Accepted: 6 APR 2012
  5. Manuscript Revised: 7 MAR 2012
  6. Manuscript Received: 25 JAN 2012

Funded by

  • BBSRC. Grant Numbers: BB/G024499/1, BB/H024654/1, BB/G024529/1

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Keywords:

  • Bioinformatics;
  • Database search;
  • Ion mobility;
  • Peptide fragmentation;
  • Peptide identification

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/.

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