Table of Contents Author Guidelines Submit a Manuscript
Advances in Bioinformatics
Volume 2013, Article ID 527295, 10 pages
http://dx.doi.org/10.1155/2013/527295
Research Article

MRMPath and MRMutation, Facilitating Discovery of Mass Transitions for Proteotypic Peptides in Biological Pathways Using a Bioinformatics Approach

1Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
2Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
3Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
4Centers for Nutrient-Gene Interactions, University of Alabama at Birmingham, Birmingham, AL 35294, USA
5Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294, USA

Received 23 September 2012; Revised 20 December 2012; Accepted 20 December 2012

Academic Editor: Erchin Serpedin

Copyright © 2013 Chiquito Crasto et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Quantitative proteomics applications in mass spectrometry depend on the knowledge of the mass-to-charge ratio (m/z) values of proteotypic peptides for the proteins under study and their product ions. MRMPath and MRMutation, web-based bioinformatics software that are platform independent, facilitate the recovery of this information by biologists. MRMPath utilizes publicly available information related to biological pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. All the proteins involved in pathways of interest are recovered and processed in silico to extract information relevant to quantitative mass spectrometry analysis. Peptides may also be subjected to automated BLAST analysis to determine whether they are proteotypic. MRMutation catalogs and makes available, following processing, known (mutant) variants of proteins from the current UniProtKB database. All these results, available via the web from well-maintained, public databases, are written to an Excel spreadsheet, which the user can download and save. MRMPath and MRMutation can be freely accessed. As a system that seeks to allow two or more resources to interoperate, MRMPath represents an advance in bioinformatics tool development. As a practical matter, the MRMPath automated approach represents significant time savings to researchers.