ABSRACT 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 AP-MS data, and all types of shotgun proteomics MS data in general. We have previously developed the Statistical Analysis of INTeractomes (SAINT) framework and a suite of tools for scoring protein interactions in AP-MS studies. We have led an international consortium to comprehensively catalogue the non-specific binding proteins observed in AP-MS experiments, establishing the Contaminant Repository for Affinity Purification (CRAPome). These and other tools developed as part of this project are now used by hundreds of laboratories worldwide. Building upon these advances, we have recently initiated the development of a comprehensive computational resource REPRINT that allows biologist to process their own AP-MS data and to visualize and interactive explore the resulting interaction networks in the context of previously known interactions, pathways, and functional categories. We will further develop this resource, including implementation of advanced network visualization options and methods for integration of user-uploaded experimental AP-MS data with external information. Furthermore, we have recently developed a new data indexing algorithm that enables ultrafast and comprehensive analysis of tandem mass spectra. We will develop a comprehensive computational workflow that will help to shine the light on the ?dark matter? of proteomics by enabling unrestricted identification of peptides with different chemical and post-translational modifications (PTMs) in AP-MS datasets. Thus, this work will add a new PTM dimension to the analysis of AP-MS interactome data. This will improve the analysis of AP-MS data by allowing more accurate quantification and detection of interacting partners. It will also allow detection of biologically important PTMs (including rare PTMs) on highly enriched bait proteins and their key interactors, which in turn will assist with uncovering the role of those PTMs on the dynamic and condition-specific interactomes. 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.

Public Health Relevance

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. This work will also add a new PTM (post- translational modifications) dimension to the analysis of AP-MS interactome data. All computational tools developed as a part of this proposal will be made freely available to the research community.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM094231-11
Application #
10016336
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Ravichandran, Veerasamy
Project Start
2010-09-27
Project End
2022-08-31
Budget Start
2020-09-01
Budget End
2021-08-31
Support Year
11
Fiscal Year
2020
Total Cost
Indirect Cost
Name
University of Michigan Ann Arbor
Department
Pathology
Type
Schools of Medicine
DUNS #
073133571
City
Ann Arbor
State
MI
Country
United States
Zip Code
48109
Feltham, Rebecca; Jamal, Kunzah; Tenev, Tencho et al. (2018) Mind Bomb Regulates Cell Death during TNF Signaling by Suppressing RIPK1's Cytotoxic Potential. Cell Rep 23:470-484
Anwar, Talha; Arellano-Garcia, Caroline; Ropa, James et al. (2018) p38-mediated phosphorylation at T367 induces EZH2 cytoplasmic localization to promote breast cancer metastasis. Nat Commun 9:2801
Hawkins, Allegra G; Basrur, Venkatesha; da Veiga Leprevost, Felipe et al. (2018) The Ewing Sarcoma Secretome and Its Response to Activation of Wnt/beta-catenin Signaling. Mol Cell Proteomics 17:901-912
Ropa, James; Saha, Nirmalya; Chen, Zhiling et al. (2018) PAF1 complex interactions with SETDB1 mediate promoter H3K9 methylation and transcriptional repression of Hoxa9 and Meis1 in acute myeloid leukemia. Oncotarget 9:22123-22136
Avtonomov, Dmitry M; Polasky, Daniel A; Ruotolo, Brandon T et al. (2018) IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry. Anal Chem 90:2369-2375
Khoriaty, Rami; Hesketh, Geoffrey G; Bernard, Amélie et al. (2018) Functions of the COPII gene paralogs SEC23A and SEC23B are interchangeable in vivo. Proc Natl Acad Sci U S A 115:E7748-E7757
Xu, Tao; Park, Sung-Soo; Giaimo, Benedetto Daniele et al. (2017) RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1. EMBO J 36:3232-3249
Meyer, Jesse G; Mukkamalla, Sushanth; Steen, Hanno et al. (2017) PIQED: automated identification and quantification of protein modifications from DIA-MS data. Nat Methods 14:646-647
Rolland, Delphine C M; Basrur, Venkatesha; Jeon, Yoon-Kyung et al. (2017) Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas. Proc Natl Acad Sci U S A 114:6581-6586
Bruderer, Roland; Sondermann, Julia; Tsou, Chih-Chiang et al. (2017) New targeted approaches for the quantification of data-independent acquisition mass spectrometry. Proteomics 17:

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