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Bioinformatics for Omics Data

Volume 719 of the series Methods in Molecular Biology pp 331-349

Date:

Bioinformatics for Qualitative and Quantitative Proteomics

  • Chris BielowAffiliated withAG Algorithmische Bioinformatik, Institut für Informatik, Freie Universität Berlin Email author 
  • , Clemens GröplAffiliated withErnst-Moritz-Arndt-Universität Greifswald
  • , Oliver KohlbacherAffiliated withEberhard-Karls-Universität Tübingen
  • , Knut ReinertAffiliated withAG Algorithmische Bioinformatik, Institut für Informatik, Freie Universität Berlin

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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