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Article

DBParser: Web-Based Software for Shotgun Proteomic Data Analyses

Supporting Info

Xiaoyu Yang,^† Vijay Dondeti,^† Rebecca Dezube,^‡ Dawn M. Maynard,^† Lewis Y. Geer,^§ Jonathan Epstein,^‡ Xiongfong Chen,^‡ Sanford P. Markey,^† and Jeffrey A. Kowalak*^†

National Institutes of Health, 10 Center Drive, Room 3D42, Bethesda, Maryland 20892-1262

Journal of Proteome Research, 2004, 3 (5), pp 1002–1008

DOI: 10.1021/pr049920x

Publication Date (Web): September 18, 2004

†

Laboratory of Neurotoxicology, National Institute of Mental Health.

‡

Unit on Biologic Computation, National Institute of Child Health and Human Development.

National Center for Biotechnology Information, National Library of Medicine.

To whom correspondence should be addressed. Tel: (301) 496 4242. Fax: (301) 480 0198. Email: jeffrey.kowalak@nih.gov.

Abstract

We describe a web-based program called ‘DBParser' for rapidly culling, merging, and comparing sequence search engine results from multiple LC−MS/MS peptide analyses. DBParser employs the principle of parsimony to consolidate redundant protein assignments and derive the most concise set of proteins consistent with all of the assigned peptide sequences observed in an experiment or series of experiments. The resulting reports summarize peptide and protein identifications from multidimensional experiments that may contain a single data set or combine data from a group of data sets, all related to a single analytical sample. Additionally, the results of multiple experiments, each of which may contain several data sets, can be compared in reports that identify features that are common or different. DBParser actively links to the primary mass spectral data and to public online databases such as NCBI, GO, and Swiss-Prot in order to structure contextually specific reports for biologists and biochemists.

Keywords: proteomics • data analysis • peptides • mass spectrometry • software • bioinformatics

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