MASCOT HTML and XML parser: An implementation of a novel object model for protein identification data

Chunguang G. Yang, Stephen J. Granite, Jennifer E. Van Eyk, Raimond L. Winslow

Research output: Contribution to journalArticle

Abstract

Protein identification using MS is an important technique in proteomics as well as a major generator of proteomics data. We have designed the protein identification data object model (PDOM) and developed a parser based on this model to facilitate the analysis and storage of these data. The parser works with HTML or XML files saved or exported from MASCOT MS/MS ions search in peptide summary report or MASCOT PMF search in protein summary report. The program creates PDOM objects, eliminates redundancy in the input file, and has the capability to output any PDOM object to a relational database. This program facilitates additional analysis of MASCOT search results and aids the storage of protein identification information. The implementation is extensible and can serve as a template to develop parsers for other search engines. The parser can be used as a stand-alone application or can be driven by other Java programs. It is currently being used as the front end for a system that loads HTML and XML result files of MASCOT searches into a relational database. The source code is freely available at http:// www.ccbm.jhu.edu and the program uses only free and open-source Java libraries.

Original languageEnglish (US)
Pages (from-to)5688-5693
Number of pages6
JournalProteomics
Volume6
Issue number21
DOIs
StatePublished - Nov 1 2006

Keywords

  • HTML parser
  • Java
  • MASCOT parser
  • Protein identification data object model
  • XML parser

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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