title: From pull-down data to protein interaction networks and complexes with biological relevance.
abstract: BACKGROUND
  Recent improvements in high-throughput Mass Spectrometry (MS) technology have expedited genome-wide discovery of protein-protein interactions by providing a capability of detecting protein complexes in a physiological setting. Computational inference of protein interaction networks and protein complexes from MS data are challenging. Advances are required in developing robust and seamlessly integrated procedures for assessment of protein-protein interaction affinities, mathematical representation of protein interaction networks, discovery of protein complexes and evaluation of their biological relevance.
  
  
  RESULTS
  A multi-step but easy-to-follow framework for identifying protein complexes from MS pull-down data is introduced. It assesses interaction affinity between two proteins based on similarity of their co-purification patterns derived from MS data. It constructs a protein interaction network by adopting a knowledge-guided threshold selection method. Based on the network, it identifies protein complexes and infers their core components using a graph-theoretical approach. It deploys a statistical evaluation procedure to assess biological relevance of each found complex. On Saccharomyces cerevisiae pull-down data, the framework outperformed other more complicated schemes by at least 10% in F(1)-measure and identified 610 protein complexes with high-functional homogeneity based on the enrichment in Gene Ontology (GO) annotation. Manual examination of the complexes brought forward the hypotheses on cause of false identifications. Namely, co-purification of different protein complexes as mediated by a common non-protein molecule, such as DNA, might be a source of false positives. Protein identification bias in pull-down technology, such as the hydrophilic bias could result in false negatives.
authors.affiliation: Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
authors.forename: Byung-Hoon
authors.initials: BH
authors.lastname: Park
authors.forename: Tatiana
authors.initials: T
authors.lastname: Karpinets
authors.forename: Nagiza F
authors.initials: NF
authors.lastname: Samatova
mesh_terms: D000465:Algorithms; D001695:Biology / Q000379:methods; D003198:Computer Simulation; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D008954:Models, Biological; D010449:Peptide Mapping / Q000379:methods; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D013329:Structure-Activity Relationship; D018511:Systems Integration
chemical_list: D011506:Proteins