scholarly journals Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

PROTEOMICS ◽  
2012 ◽  
Vol 12 (10) ◽  
pp. 1639-1655 ◽  
Author(s):  
Alexey I. Nesvizhskii
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Affinity Purification ◽  
Specific Protein ◽  
Interaction Partners ◽  
Affinity Purification Mass Spectrometry

scholarly journals Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

2008 ◽  
Vol 183 (2) ◽  
pp. 223-239 ◽  
Author(s):  
Laura Trinkle-Mulcahy ◽  
Séverine Boulon ◽  
Yun Wah Lam ◽  
Roby Urcia ◽  
François-Michel Boisvert ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Cell Biology ◽  
Protein Complexes ◽  
Affinity Purification ◽  
Specific Protein ◽  
Protein Interaction Data ◽  
Quantitative Mass Spectrometry ◽  
Cell Extracts ◽  
Interaction Partners

The identification of interaction partners in protein complexes is a major goal in cell biology. Here we present a reliable affinity purification strategy to identify specific interactors that combines quantitative SILAC-based mass spectrometry with characterization of common contaminants binding to affinity matrices (bead proteomes). This strategy can be applied to affinity purification of either tagged fusion protein complexes or endogenous protein complexes, illustrated here using the well-characterized SMN complex as a model. GFP is used as the tag of choice because it shows minimal nonspecific binding to mammalian cell proteins, can be quantitatively depleted from cell extracts, and allows the integration of biochemical protein interaction data with in vivo measurements using fluorescence microscopy. Proteins binding nonspecifically to the most commonly used affinity matrices were determined using quantitative mass spectrometry, revealing important differences that affect experimental design. These data provide a specificity filter to distinguish specific protein binding partners in both quantitative and nonquantitative pull-down and immunoprecipitation experiments.

scholarly journals SAINT: probabilistic scoring of affinity purification–mass spectrometry data

2010 ◽  
Vol 8 (1) ◽  
pp. 70-73 ◽  
Author(s):  
Hyungwon Choi ◽  
Brett Larsen ◽  
Zhen-Yuan Lin ◽  
Ashton Breitkreutz ◽  
Dattatreya Mellacheruvu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Affinity Purification ◽  
Mass Spectrometry Data ◽  
Affinity Purification Mass Spectrometry
Sign in / Sign up

Export Citation Format

Share Document