Scripps VIVO scripps research logo

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

Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra

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

Overview

authors

  • Venable, J. D.
  • Dong, M. Q.
  • Wohlschlegel, J.
  • Dillin, A.
  • Yates III, John

publication date

  • October 2004

journal

  • Nature Methods  Journal

abstract

  • To take advantage of the potential quantitative benefits offered by tandem mass spectrometry, we have modified the method in which tandem mass spectrum data are acquired in 'shotgun' proteomic analyses. The proposed method is not data dependent and is based on the sequential isolation and fragmentation of precursor windows (of 10 m/z) within the ion trap until a desired mass range has been covered. We compared the quantitative figures of merit for this method to those for existing strategies by performing an analysis of the soluble fraction of whole-cell lysates from yeast metabolically labeled in vivo with (15)N. To automate this analysis, we modified software (RelEx) previously written in the Yates lab to generate chromatograms directly from tandem mass spectra. These chromatograms showed improvements in signal-to-noise ratio of approximately three- to fivefold over corresponding chromatograms generated from mass spectrometry scans. In addition, to demonstrate the utility of the data-independent acquisition strategy coupled with chromatogram reconstruction from tandem mass spectra, we measured protein expression levels in two developmental stages of Caenorhabditis elegans.

subject areas

  • Algorithms
  • Animals
  • Caenorhabditis elegans
  • Caenorhabditis elegans Proteins
  • Cells, Cultured
  • Chromatography
  • Complex Mixtures
  • Gene Expression Regulation, Developmental
  • Peptides
  • Proteomics
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Analysis, Protein
  • Spectrometry, Mass, Electrospray Ionization
scroll to property group menus

Identity

International Standard Serial Number (ISSN)

  • 1548-7091

Digital Object Identifier (DOI)

  • 10.1038/nmeth705

PubMed ID

  • 15782151
scroll to property group menus

Additional Document Info

start page

  • 39

end page

  • 45

volume

  • 1

issue

  • 1

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

  • About
  • Contact Us
  • Support