Subtle modification of isotope ratio proteomics; An integrated strategy for expression proteomics

Julian P. Whitelegge, Jonathan E. Katz, Katianna A. Pihakari, Rebecca Hale, Rodrigo Aguilera, Stephen M. Gómez, Kym F. Faull, Dmitrii Vavilin, Willem Vermaas

Research output: Contribution to journalArticlepeer-review

53 Scopus citations


Use of minor modification of isotope ratio to code samples for expression proteomics is being investigated. Alteration of 13C abundance to ∼2% yields a measurable effect on peptide isotopic distribution and inferred isotope ratio. Elevation of 13C abundance to 4% leads to extension of isotopic distribution and background peaks across every unit of the mass range. Assessment of isotope ratio measurement variability suggests substantial contributions from natural measurement variability. A better understanding of this variable will allow assessment of the contribution of sequence dependence. Both variables must be understood before meaningful mixing experiments for relative expression proteomics are performed. Subtle modification of isotope ratio (∼1-2% increase in 13C) had no effect upon either the ability of data-dependent acquisition software or database searching software to trigger tandem mass spectrometry or match MSMS data to peptide sequences. More severe modification of isotope ratio caused a significant drop in performance of both functionalities. Development of software for deconvolution of isotope ratio concomitant with protein identification using LC-MSMS, or any other proteomics strategy, is underway (Isosolv). The identified peptide sequence is then be used to provide elemental composition for accurate isotope ratio decoding and the potential to control for specific amino acid biases should these prove significant. It is suggested that subtle modification of isotope ratio proteomics (SMIRP) offers a convenient approach to in vivo isotope coding of plants and might ultimately be extended to mammals including humans.

Original languageEnglish (US)
Pages (from-to)1507-1515
Number of pages9
Issue number11
StatePublished - Jun 2004


  • Cyanobacteria
  • Isotope coding
  • Proteome
  • Proteomics
  • Stable isotopes
  • Synechocystis sp. PCC 6803

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Plant Science
  • Horticulture


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