Bioinformatics for Qualitative and Quantitative Proteomics

  • Chris Bielow
  • Clemens Gröpl
  • Oliver Kohlbacher
  • Knut Reinert
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 719)

Abstract

Mass spectrometry is today a key analytical technique to elucidate the amount and content of proteins expressed in a certain cellular context. The degree of automation in proteomics has yet to reach that of genomic techniques, but even current technologies make a manual inspection of the data infeasible. This article addresses the key algorithmic problems bioinformaticians face when handling modern proteomic samples and shows common solutions to them. We provide examples on how algorithms can be combined to build relatively complex analysis pipelines, point out certain pitfalls and aspects worth considering and give a list of current state-of-the-art tools.

Key words

Mass Spectrometry MALDI ESI HPLC MS MS/MS Tandem-MS Software Algorithm 

Notes

Acknowledgments

CB is supported by the European Commission´s 7th Framework Program (GA202222). OK gratefully acknowledges financial support from DFG (SFB 685/B1, SPP 1335) and BMBF (0313842A, 0315395F).

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Chris Bielow
    • 1
  • Clemens Gröpl
    • 2
  • Oliver Kohlbacher
    • 3
  • Knut Reinert
    • 1
  1. 1.AG Algorithmische Bioinformatik, Institut für InformatikFreie Universität BerlinBerlinGermany
  2. 2.Ernst-Moritz-Arndt-Universität GreifswaldGreifswaldGermany
  3. 3.Eberhard-Karls-Universität TübingenTübingenGermany

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