Editing Proteomics (section)

===Interaction proteomics and protein networks===
Interaction proteomics is the analysis of protein interactions from scales of binary interactions to proteome- or network-wide.  Most proteins function via [[protein–protein interaction]]s, and one goal of interaction proteomics is to [[Methods to investigate protein-protein interactions|identify binary protein interactions]], [[multiprotein complex|protein complexes]], and [[interactome]]s.

Several methods are available to [[Methods to investigate protein-protein interactions|probe protein–protein interactions]]. While the most traditional method is yeast [[Two-hybrid screening|two-hybrid analysis]], a powerful emerging method is [[co-immunoprecipitation|affinity purification]] followed by [[protein mass spectrometry]] using [[protein tag|tagged protein baits]]. Other methods include [[surface plasmon resonance]] (SPR),<ref>{{cite book | vauthors = de Mol NJ | chapter = Surface Plasmon Resonance for Proteomics | title = Chemical Genomics and Proteomics | series = Methods in Molecular Biology | volume = 800 | pages = 33–53 | date = 2012 | pmid = 21964781 | doi = 10.1007/978-1-61779-349-3_4 | isbn = 978-1-61779-348-6 }}</ref><ref>{{cite journal | vauthors = Visser NF, Heck AJ | title = Surface plasmon resonance mass spectrometry in proteomics | journal = Expert Review of Proteomics | volume = 5 | issue = 3 | pages = 425–433 | date = June 2008 | pmid = 18532910 | doi = 10.1586/14789450.5.3.425 | s2cid = 11772983 }}</ref> [[protein microarray]]s, [[dual polarisation interferometry]], [[microscale thermophoresis]], [[kinetic exclusion assay]], and experimental methods such as [[phage display]] and ''in silico'' computational methods.

Knowledge of protein-protein interactions is especially useful in regard to [[biological network]]s and [[systems biology]], for example in [[cell signaling]] cascades and [[gene regulatory network]]s (GRNs, where knowledge of [[transcription factor|protein-DNA interactions]] is also informative). Proteome-wide analysis of protein interactions, and integration of these interaction patterns into larger [[biological network]]s, is crucial towards understanding [[#Proteomics for systems biology|systems-level biology]].<ref name="Bensimon_2012">{{cite journal | vauthors = Bensimon A, Heck AJ, Aebersold R | title = Mass spectrometry-based proteomics and network biology | journal = Annual Review of Biochemistry | volume = 81 | issue = 1 | pages = 379–405 | date = 7 July 2012 | pmid = 22439968 | doi = 10.1146/annurev-biochem-072909-100424 }}</ref><ref name="Sabidó_2012">{{cite journal | vauthors = Sabidó E, Selevsek N, Aebersold R | title = Mass spectrometry-based proteomics for systems biology | journal = Current Opinion in Biotechnology | volume = 23 | issue = 4 | pages = 591–597 | date = August 2012 | pmid = 22169889 | doi = 10.1016/j.copbio.2011.11.014 }}</ref>