title: Protein complex analysis: From raw protein lists to protein interaction networks.
abstract: The elucidation of molecular interaction networks is one of the pivotal challenges in the study of biology. Affinity purification-mass spectrometry and other co-complex methods have become widely employed experimental techniques to identify protein complexes. These techniques typically suffer from a high number of false negatives and false positive contaminants due to technical shortcomings and purification biases. To support a diverse range of experimental designs and approaches, a large number of computational methods have been proposed to filter, infer and validate protein interaction networks from experimental pull-down MS data. Nevertheless, this expansion of available methods complicates the selection of the most optimal ones to support systems biology-driven knowledge extraction. In this review, we give an overview of the most commonly used computational methods to process and interpret co-complex results, and we discuss the issues and unsolved problems that still exist within the field. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:600-614, 2017.
authors.affiliation: Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.|Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium.
authors.forename: Pieter
authors.initials: P
authors.lastname: Meysman
authors.affiliation: Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium.|Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
authors.forename: Kevin
authors.initials: K
authors.lastname: Titeca
authors.affiliation: Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium.|Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
authors.forename: Sven
authors.initials: S
authors.lastname: Eyckerman
authors.affiliation: Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium.|Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Tavernier
authors.affiliation: Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.
authors.forename: Bart
authors.initials: B
authors.lastname: Goethals
authors.affiliation: Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium.|Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.affiliation: Flemish Institute for Technological Research (VITO), Mol, Belgium.|IBioStat, Hasselt University, Hasselt, Belgium.|CFP-CeProMa, University of Antwerp, Antwerp, Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Valkenborg
authors.affiliation: Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.|Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium.
authors.forename: Kris
authors.initials: K
authors.lastname: Laukens
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D046912:Multiprotein Complexes / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods* / Q000592:standards; D060066:Protein Interaction Maps; D011506:Proteins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D011786:Quality Control; D015203:Reproducibility of Results; D057188:Workflow
chemical_list: D046912:Multiprotein Complexes; D011506:Proteins
keywords: bioinformatics; co-complex purification; protein-protein interaction networks