Mass spectrometry-based label free quantification of gel separated proteins

Zoltan Szabo, Judit Szeline Szomor, Istvan Foeldi, T. Janáky

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Co-migrating proteins in 2D PAGE spots cause difficulties in the assignment of quantitative data obtained from the staining density of a gel spot. We present an application of a label free LC-MS quantitative method that can overcome problems like this. Protein mixtures were prepared with varying compositions, and were run on either 1D or 2D PAGE. Relative and absolute quantitative evaluation was carried out using a simple but reliable method based on integrated MS signals of the three most intensive peptides of each protein. The efficacy of digestion and peptide extraction is, however, influenced by different factors in gel from those in solution, hence the method had to be validated via a quantitative assessment of proteins from 1D or 2D gels. Our findings suggest that a reliable relative quantification is viable using peptide ion intensities when protein levels in two gels have to be compared. In the case of 2D gels, label free MS quantification provides more precise results on changes of protein expression levels than gel spot intensity-based measurements, especially in the case of overlapping proteins. Absolute amounts of different proteins in 1D or 2D gels can be evaluated to a reasonable precision.

Original languageEnglish
Pages (from-to)5544-5553
Number of pages10
JournalJournal of Proteomics
Volume75
Issue number18
DOIs
Publication statusPublished - Oct 22 2012

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Mass spectrometry
Labels
Mass Spectrometry
Gels
Proteins
Electrophoresis, Gel, Two-Dimensional
Peptides
Digestion
Ions
Staining and Labeling
Chemical analysis

Keywords

  • 2DGE
  • Label free
  • Quantification

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics

Cite this

Mass spectrometry-based label free quantification of gel separated proteins. / Szabo, Zoltan; Szomor, Judit Szeline; Foeldi, Istvan; Janáky, T.

In: Journal of Proteomics, Vol. 75, No. 18, 22.10.2012, p. 5544-5553.

Research output: Contribution to journalArticle

Szabo, Zoltan ; Szomor, Judit Szeline ; Foeldi, Istvan ; Janáky, T. / Mass spectrometry-based label free quantification of gel separated proteins. In: Journal of Proteomics. 2012 ; Vol. 75, No. 18. pp. 5544-5553.
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