The analysis of protein complexes and interaction networks, and their dynamic behavior are of central importance in biological research. Affinity purification coupled with mass spectrometry (AP-MS) is now widely used for protein interaction analysis. Our work addresses the critical need to develop robust computational methods and tools for these data. We have demonstrated the great utility of label-free quantitative protein abundance information that can be extracted from AP-MS data, and developed the Statistical Analysis of INTeractomes (SAINT) framework for scoring protein interactions in AP-MS studies. We have also initiated an international consortium to comprehensively catalogue the non-specific binding proteins observed in AP-MS experiments - the Contaminant Repository for Affinity Purification (CRAPome.org). Building upon these advances, we will continue toward our goal of developing a comprehensive computational resource for scoring protein interaction data applicable to most commonly used experimental protocols and MS platforms. We will also gain a better understanding of the underlying mechanisms of non-specific binding - generating knowledge useful both for retrospective analysis of previously published data and for the design of future experiments. By integrating the experimental AP-MS data with external information such as structure-based protein interaction predictions, we will further improve the sensitivity of detection of low abundance and transient interactions. It has also become apparent that charting a complete interaction map for an organism like human is a community-wide effort, with multiple groups contributing separate portions of the entire interactome. We will develop a novel computational framework for consistent integration of AP-MS datasets from different studies, leading to more complete and accurate quantitative interaction networks. Lastly, one important problem that has yet to be fully addressed is the quantitative analysis protein complexes and interaction networks dynamics. The emergence of highly sensitive multiplex MS techniques presents such an opportunity, and we will develop advanced computational algorithms and tools for differential and dynamic interactome analysis using multiplex MS data. We will continue providing our widely used computational tools and data resources to the biological community, along with benchmark datasets for further development of computational methods by other scientists.
The proposed computational work will enable statistically robust and quantitative analysis of protein-protein interactions and protein complexes using affinity purification - mass spectrometry (AP/MS) approach. The bioinformatics methods will allow establishing a computational framework for quality assessment, analysis, modelling, and cross-laboratory comparison of AP/MS data. The tools and methods will be of great utility for both large collaborative interactome projects and small scale studies. All computational tools developed as a part of this proposal will be made freely available to the research community.
|Lambert, Jean-Philippe; Tucholska, Monika; Go, Christopher et al. (2015) Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. J Proteomics 118:81-94|
|Lambert, Jean-Philippe; Tucholska, Monika; Pawson, Tony et al. (2014) Incorporating DNA shearing in standard affinity purification allows simultaneous identification of both soluble and chromatin-bound interaction partners. J Proteomics 100:55-9|
|Nesvizhskii, Alexey I (2014) Proteogenomics: concepts, applications and computational strategies. Nat Methods 11:1114-25|
|Rolland, Delphine; Basrur, Venkatesha; Conlon, Kevin et al. (2014) Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas. Am J Pathol 184:1331-42|
|Johnson, Cole; Kweon, Hye Kyong; Sheidy, Daniel et al. (2014) The yeast Sks1p kinase signaling network regulates pseudohyphal growth and glucose response. PLoS Genet 10:e1004183|
|Shanmugam, Avinash K; Yocum, Anastasia K; Nesvizhskii, Alexey I (2014) Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS. J Proteome Res 13:4113-9|
|Teo, Guoci; Liu, Guomin; Zhang, Jianping et al. (2014) SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software. J Proteomics 100:37-43|
|Taipale, Mikko; Tucker, George; Peng, Jian et al. (2014) A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways. Cell 158:434-48|
|Kao, S-H; Wang, W-L; Chen, C-Y et al. (2014) GSK3* controls epithelial-mesenchymal transition and tumor metastasis by CHIP-mediated degradation of Slug. Oncogene 33:3172-82|
|Mellacheruvu, Dattatreya; Wright, Zachary; Couzens, Amber L et al. (2013) The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods 10:730-6|
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