Systems BIOLOGY "on-the-fly": SILAC-based quantitative proteomics and RNAI approach in drosophila melanogaster

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Stable isotope labeling with amino acids in cell culture (SILAC) has become increasingly popular as a quantitative proteomics (qProteomics) method. In combination with high-resolution mass spectrometry (MS) and new efficient algorithms for the analysis of quantitative MS data, SILAC has proven to be a potent tool for the in-depth characterization of functional states. QProteomics extends transcriptomics analysis in providing comprehensive and unbiased protein expression profiles. In this chapter, we describe the use of SILAC procedure in combination with RNA interference (RNAi) to characterize loss-of-function phenotypes, an example to illustrate how qProteomics can address many of the systems-wide approaches previously restricted to the mRNA level. Furthermore, by explaining the adaptation of SILAC to a novel cellular model, the Drosophila melanogaster Schneider cells SL2, we aim to offer an example enabling the readers to apply the same strategy to any other cell culture, specific for their need.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages59-78
Number of pages20
Volume662
ISBN (Print)9781607617990
DOIs
Publication statusPublished - 2010

Publication series

NameMethods in Molecular Biology
Volume662
ISSN (Print)10643745

Keywords

  • Mass spectrometry
  • MaxQuant
  • Orbitrap
  • Quantitative proteomics
  • RNA interference
  • Schneider cells
  • SILAC

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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