Volume 30, Issue 2 p. 268-297

Linking the proteins—Elucidation of proteome-scale networks using mass spectrometry

Delphine Pflieger

Delphine Pflieger

Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, CNRS UMR 8587, Evry, France

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Florence Gonnet

Florence Gonnet

Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, CNRS UMR 8587, Evry, France

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Sergio de la Fuente van Bentem

Sergio de la Fuente van Bentem

Syngenta Seeds B.V., P.O. Box 2, 1600 AA Enkhuizen, the Netherlands

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Heribert Hirt

Heribert Hirt

URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, F-91057, France

MFPL, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria

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Alberto de la Fuente

Corresponding Author

Alberto de la Fuente

CRS4 Bioinformatica, c/o Parco Tecnologico POLARIS, Edificio 1, Loc. Piscina Manna, 09010 Pula, Italy

CRS4 Bioinformatica, c/o Parco Tecnologico POLARIS, Edificio 1, Loc. Piscina Manna, 09010 Pula, Italy.Search for more papers by this author
First published: 17 February 2011
Citations: 23

Abstract

Proteomes are intricate. Typically, thousands of proteins interact through physical association and post-translational modifications (PTMs) to give rise to the emergent functions of cells. Understanding these functions requires one to study proteomes as “systems” rather than collections of individual protein molecules. The abstraction of the interacting proteome to “protein networks” has recently gained much attention, as networks are effective representations, that lose specific molecular details, but provide the ability to see the proteome as a whole. Mostly two aspects of the proteome have been represented by network models: proteome-wide physical protein–protein-binding interactions organized into Protein Interaction Networks (PINs), and proteome-wide PTM relations organized into Protein Signaling Networks (PSNs). Mass spectrometry (MS) techniques have been shown to be essential to reveal both of these aspects on a proteome-wide scale. Techniques such as affinity purification followed by MS have been used to elucidate protein–protein interactions, and MS-based quantitative phosphoproteomics is critical to understand the structure and dynamics of signaling through the proteome. We here review the current state-of-the-art MS-based analytical pipelines for the purpose to characterize proteome-scale networks. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:268–297, 2011