Protein complex analysis : from raw protein lists to protein interaction networks
Faculty of Sciences. Biology
Faculty of Sciences. Chemistry
Faculty of Sciences. Mathematics and Computer Science
Faculty of Pharmaceutical, Biomedical and Veterinary Sciences . Biomedical Sciences
New York, N.Y.
Mass spectrometry reviews. - New York, N.Y., 1982, currens
, p. 1-15
University of Antwerp
The elucidation of molecular interaction networks is one of the pivotal challenges in the study of biology. Affinity purificationmass 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 9999: XXXX, 2015.