Awsome affinity purification mass spectrometry (AP-MS)

Jul 8, 2018 2 min read Awsome

A collection of resources regarding affinity purification mass spectrometry proteomics for the identification of protein-protein interactions.

Algorithms

Year	Algorithm	Publication	Implementation
2006	SAI (socio-affinity index)	Anne-Claude Gavin et al., Nature
2007	partial least squares based regression model	Rob M Ewing et al., Mol Syst Biol
2007	PE (purification enrichment)	Sean R. Collins et al., Molecular & Cellular Proteomics	SMAD
2007	Hart	G Traver Hart et al., BMC Bioinformatics	SMAD
2008	Dice coefficient	Bing Zhang et al., Bioinformatics	SMAD
2008	PP-NSAF	Mihaela E. Sardiu et al., PNAS
2009	CompPASS	Mathew E.Sowa et al., Cell	SMAD
2010	Decontaminator	MathieLavallée-Adam et al. J. Proteome Res.
2011	MiST	Stefanie Jäger et al., Nature	mist
2011	HGScore	K.G.Guruharsha et al., Cell	SMAD
2011	SAINT	Hyungwon Choi et al., Nature Methods	SAINT
2015	SFINX	Kevin Titeca et al. J. Proteome Res.	SFINX

Datasets

Year	Species	Abstract	Publication
2002	S.cerevisiae	725 bait proteins, one-step immuno-affinity purification based on the Flag epitope tag	Yuen Ho et al., Nature
2002	S.cerevisiae	tandem-affinity purification processed 1,739 genes	Anne-Claude Gavin et al., Nature
2006	S.cerevisiae	Genome-wide TAP–MS, first introduced	Anne-Claude Gavin et al., Nature
2009	H.sapiens	Human Deubiquitinating Enzyme Interaction Landscape(DUB)	Mathew E.Sowa et al., Cell
2010	S.cerevisiae	kinase and phosphatase interaction (KPI) network	Ashton Breitkreutz et al., Science
2009	H.sapiens	autophagy interaction network (AIN)	Christian Behrends et al., Nature
2011	D.melanogaster	a Drosophila protein interaction map (DPiM)	K.G.Guruharsha et al., Cell
2012	S.cerevisiae	membrane-protein complexes in yeast	Mohan Babu et al., Nature
2014	H.sapiens	A comprehensive chromatin-related protein-protein interaction map	Edyta Marcon et al., Cell Reports
2015	H.sapiens	BioPlex v1	Edward L. Huttlin et al., Cell
2015	H.sapiens	Autism Spectrum Disorders related	Jingjing Li et al., Cell Systems
2016	H.sapiens	PPI mapping of 50 unannotated mitochondrial proteins	Brendan J.Floyd et al., Molecular Cell
2016	H.sapiens	Comprehensive mitochondrial sirtuin interactome	Wen Yang et al., Cell
2017	H.sapiens	BioPlex v2	Edward L. Huttlin et al., Cell
2017	E.coli	Global landscape of cell envelope protein complexes	Mohan Babu et al., Nature Biotech
2017	H.sapiens	A Map of Human Mitochondrial Protein Interactions related to Neurodegeneration	Ramy H.Malty et al., Cell Systems

AP-MS Interactome