alexa ModLS: Post-Translational Modification Localization Sco
ISSN: 0974-276X

Journal of Proteomics & Bioinformatics
Open Access

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Research Article

ModLS: Post-Translational Modification Localization Scoring with Automatic Specificity Expansion

David C. Trudgian1,2*, Rachelle Singleton2, Matthew E. Cockman2, Peter. J. Ratcliffe2 and Benedikt M. Kessler2

1Proteomics Core, Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX 75390-8816, USA

2Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK

*Corresponding Author:
David C. Trudgian
Proteomics Core, Department of Biochemistry
University of Texas Southwestern Medical Center at Dallas
6001 Forest Park Rd
Dallas, TX 75390-8816, USA
Tel: +1 214-648-7025
Fax: +1 214-645-5961
E-mail: [email protected]

Received Date: December 04, 2012; Accepted Date: December 27, 2012; Published Date: December 29, 2012

Citation: Trudgian DC, Singleton R, Cockman ME, Ratcliffe PJ, Kessler BM (2012) ModLS: Post-Translational Modification Localization Scoring with Automatic Specificity Expansion. J Proteomics Bioinform 5: 283-289. doi: 10.4172/jpb.1000251

Copyright: © 2012 Trudgian DC, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

 

Abstract

Probability-based localisation scoring of fragment mass-spectrum phosphorylation site identifications has become common practice to confirm search engine modification assignments, and indicate the degree of certainty with which they are defined. Localisation of modifications other than phosphorylation is also required but is less commonly supported by current tools. These other modifications, such as hydroxylation, may have broad aminoacid specificity, and can be misassigned when the correct specificity is not considered in an MS database search. In addition, localisation software is often specific to a particular MS/MS search engine, and cannot be used to localise modifications identified by multiple search engines. ModLS, a new tool within our freely-available Central Proteomics Facilities Pipeline (CPFP), applies a localisation scoring method to arbitrary post-translational modifications (PTMs). As well as localising PTMs based on amino-acid specificities are included in the initial search, ModLS can automatically consider additional specificities from UniMod. This can help avoid ‘correct modification, incorrect amino-acid’ errors which can occur when data is searched using only a subset of PTM specificities. Localisation scoring can be performed on the results from any search engine incorporated within the pipeline, or where the output of individual search engines is combined to give increased coverage. We demonstrate the performance of ModLS using a publicly available phosphorylated peptide dataset, showing that it outperforms the recently characterised Mascot Delta Score approach for CID and MSA data, and is comparable for HCD data. In addition, we show the utility of automatic specificity expansion using hydroxylated and methylated peptide data. ModLS is a user-friendly localisation tool for arbitrary modifications. Its inclusion within CPFP allows PTM localisation to be performed quickly and easily on large or small result sets, from multiple search engines. Specificity expansion, introduced in ModLS, allows misassignments of modifications due to incomplete consideration of specificities to be identified and minimised.

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