QuantiSpec - Quantitative mass spectrometry data analysis of 15N-metabolically labeled proteins

Katrin Haegler, Nikola S. Mueller, Giuseppina Maccarrone, Eva Hunyadi-Gulyas, Christian Webhofer, Michaela D. Filiou, Yaoyang Zhang, Christoph W. Turck

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

For relative protein quantitation by mass spectrometry we metabolically labeled E. coli bacteria with 15N-enriched diets. Proteins extracted from 15N-labeled and unlabeled E. coli bacteria were mixed, separated by two-dimensional gel electrophoresis and enzymatically digested. The resulting tryptic peptides were analyzed by MALDI mass spectrometry. For the relative protein quantitation we developed fully automated software, QuantiSpec (Quantitative Mass Spectrometry Analysis Software), which uses data from MALDI TOF mass spectrometry and the Mascot database search engine. QuantiSpec detects natural as well as partially or fully labeled peptide isotope distributions. For each identified peptide the 15N incorporation rate is determined by comparing the experimental to a set of theoretical isotope patterns based on the peptide sequence. Relative quantitation is accomplished by calculating the signal intensity ratios for each 14N/15N peptide pair.

Original languageEnglish
Pages (from-to)601-608
Number of pages8
JournalJournal of proteomics
Volume71
Issue number6
DOIs
Publication statusPublished - Jan 30 2009

Keywords

  • Bioinformatics
  • Computer software
  • Fast Fourier Transform
  • Partial metabolic labeling
  • Quantitative mass spectrometry
  • Stable isotopes

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry

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    Haegler, K., Mueller, N. S., Maccarrone, G., Hunyadi-Gulyas, E., Webhofer, C., Filiou, M. D., Zhang, Y., & Turck, C. W. (2009). QuantiSpec - Quantitative mass spectrometry data analysis of 15N-metabolically labeled proteins. Journal of proteomics, 71(6), 601-608. https://doi.org/10.1016/j.jprot.2008.10.004