Scripps VIVO scripps research logo

  • Index
  • Log in
  • Home
  • People
  • Organizations
  • Research
  • Events
Search form

Searching the Porphyromonas gingivalis genome with peptide fragmentation mass spectra

Academic Article
uri icon
  • Overview
  • Identity
  • Additional Document Info
  • View All
scroll to property group menus

Overview

authors

  • Chen, W. B.
  • Laidig, K. E.
  • Park, Y.
  • Park, K.
  • Yates III, John
  • Lamont, R. J.
  • Hackett, M.

publication date

  • 2001

journal

  • Analyst  Journal

abstract

  • An approach is described for genomic database searching based on experimentally observed proteolytic fragments, e.g., isolated from 1D or 2D gels or analyzed directly, that can be applied to unfinished prokaryotic genomic data in the absence of annotations or previously assigned open reading frames (ORFs). This variation on the database search is in contrast to the more familiar use of peptide mass spectral fragmentation data to search fully annotated inferred protein databases, e.g., OWL or SWISS-PROT. We compared the SEQUEST search results from a six reading frame translation of the Porphyromonas gingivalis genome DNA sequence with those from computationally derived ORFs created using publicly available genomics software tools. The ORF approach eliminated many of the artifacts present in output from the six reading frame search. The method was applied to uninterpreted tandem mass spectrometric data derived from proteins secreted by the periodontal pathogen Porphyromonas gingivalis in response to the gingival epithelial cell environment, a model system for the study of host-pathogen interactions relevant to human periodontal disease.

subject areas

  • Bacterial Proteins
  • Cells, Cultured
  • Databases, Factual
  • Genome, Bacterial
  • Genomic Library
  • Gingiva
  • Humans
  • Information Storage and Retrieval
  • Mass Spectrometry
  • Models, Biological
  • Open Reading Frames
  • Porphyromonas gingivalis
  • Sensitivity and Specificity
scroll to property group menus

Identity

International Standard Serial Number (ISSN)

  • 0003-2654

Digital Object Identifier (DOI)

  • 10.1039/b008012h

PubMed ID

  • 11205512
scroll to property group menus

Additional Document Info

start page

  • 52

end page

  • 57

volume

  • 126

issue

  • 1

©2021 The Scripps Research Institute | Terms of Use | Powered by VIVO

  • About
  • Contact Us
  • Support