Proteomics in Systems Biology pp 261-273

Part of the Methods in Molecular Biology book series (MIMB, volume 1394) | Cite as

Interpretation of Quantitative Shotgun Proteomic Data

  • Elise Aasebø
  • Frode S. Berven
  • Frode Selheim
  • Harald Barsnes
  • Marc Vaudel
Protocol

Abstract

In quantitative proteomics, large lists of identified and quantified proteins are used to answer biological questions in a systemic approach. However, working with such extensive datasets can be challenging, especially when complex experimental designs are involved. Here, we demonstrate how to post-process large quantitative datasets, detect proteins of interest, and annotate the data with biological knowledge. The protocol presented can be achieved without advanced computational knowledge thanks to the user-friendly Perseus interface (available from the MaxQuant website, www.maxquant.org). Various visualization techniques facilitating the interpretation of quantitative results in complex biological systems are also highlighted.

Key words

Quantification Data interpretation Perseus Data post-processing 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Elise Aasebø
    • 1
  • Frode S. Berven
    • 1
    • 2
    • 3
  • Frode Selheim
    • 1
  • Harald Barsnes
    • 1
    • 4
  • Marc Vaudel
    • 1
  1. 1.Proteomics Unit, Department of BiomedicineUniversity of BergenBergenNorway
  2. 2.KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical MedicineUniversity of BergenBergenNorway
  3. 3.Norwegian Multiple Sclerosis Competence Centre, Department of NeurologyHaukeland University HospitalBergenNorway
  4. 4.KG Jebsen Center for Diabetes Research, Department of Clinical ScienceUniversity of BergenBergenNorway

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