Defects in ubiquitin (Ub) pathways are often responsible for cancer and devastating neurodegenerative diseases. Because of its central role in biological circuits and the potential for therapeutic intervention, the Ub system is an intense research area. Yet, Ub biology is highly complex?in humans it is supported by over 500 Ub ligases and 95 deubiquitinases. Currently, this complexity and our limited understanding of players and their interactions are a severe hindrance for targeted intervention in many diseases. Considering all possible ways to address the complexity, sample multiplexing in mass spectrometry-based proteomics arguably has the greatest potential to fundamentally revolutionize the throughput of these measurements. Through efforts within the previous grant cycle, the level of multiplexing was increased, facilitating the quantitative comparison of expression and conjugate levels for 10 samples. In this proposal, enabling advances in sample multiplexing will be explored and applied to study ubiquitin-dependent biology.
In Aim 1, we will evaluate isobaric reagents that have multiple reporter ions such that a 16- and a 32-plex reagent set can be synthesized using relatively few heavy atoms (4 and 6, respectively).
In Aim 2, two large obstacles to sample multiplexing will be addressed?sensitivity and proteome depth. Using a real-time database search algorithm, reporter ion quantification scans (SPS-MS3 scans) will only be collected when the MS2 scan is successfully matched to a peptide or PTM-containing peptide. This will be a very disruptive technology as MS2 scans are recorded at a blistering rate of 22 Hz. Highly optimized MS3 scans will then be collected based on any filter desired since the identity and modification state of all peptides will be known in real time. We expect dramatic improvements in the quality and depth of discovery proteomics experiments while reducing the analysis time by at least 3 fold.
In Aim 3, we will explore two new multiplexing workflows based on the technologies developed in the first two aims. One workflow will be dedicated to targeted proteomics where up to 32-plex experiments targeting hundreds of peptides will be developed. In these assays, triggering peptides and a real-time database search will obviate the need for retention time scheduling or precursor detection in survey scans prior to MS3 analysis using pre-selected SPS ions. Using panels of trigger peptides, assays to monitor the protein levels in six ubiquitin-dependent pathways will be created. The second workflow will be dedicated to discovery proteomics where up to 32-plex experiments will be conducted for full proteome or conjugate analysis in as little as 24 hr. This will be applied to characterize CRISPR deletions in the mTOR amino acid sensing pathway and specifically the mechanism of action of the GATOR2 complex where 3 ubiquitin ligases of unknown function are present. The realization of all three aims ushers in a paradigm shift in Quantitative Proteomics where hundreds to thousands of samples can be accurately compared across entire proteomes or in targeted assays in a matter of days or weeks using up to 32-plex reagent sets and real-time database searching.

Public Health Relevance

The ubiquitin system is an intense research area with great promise for the improvement of human health. In addition to its critical role in normal physiology, malfunctions in ubiquitin biology have been implicated as a contributing factor in the causation of many diseases as diverse as diabetes, cancer, and Alzheimer's disease. This proposal will develop new mass spectrometry-based technologies to allow sample multiplexing such that up to 32 clinical or experimental proteomes can be analyzed simultaneously. These technologies will revolutionize our ability to profile hundreds to thousands of individual samples within a timeframe of days or weeks, respectively. 0

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Enabling Bioanalytical and Imaging Technologies Study Section (EBIT)
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Barski, Oleg
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Harvard Medical School
Anatomy/Cell Biology
Schools of Medicine
United States
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Mills, Evanna L; Pierce, Kerry A; Jedrychowski, Mark P et al. (2018) Accumulation of succinate controls activation of adipose tissue thermogenesis. Nature 560:102-106
O'Connell, Jeremy D; Paulo, Joao A; O'Brien, Jonathon J et al. (2018) Proteome-Wide Evaluation of Two Common Protein Quantification Methods. J Proteome Res 17:1934-1942
Ordureau, Alban; Paulo, Joao A; Zhang, Wei et al. (2018) Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics. Mol Cell 70:211-227.e8
Di Stefano, Bruno; Ueda, Mai; Sabri, Shan et al. (2018) Reduced MEK inhibition preserves genomic stability in naive human embryonic stem cells. Nat Methods 15:732-740
Erickson, Brian K; Rose, Christopher M; Braun, Craig R et al. (2017) A Strategy to Combine Sample Multiplexing with Targeted Proteomics Assays for High-Throughput Protein Signature Characterization. Mol Cell 65:361-370
Lee, Ho-Joon; Jedrychowski, Mark P; Vinayagam, Arunachalam et al. (2017) Proteomic and Metabolomic Characterization of a Mammalian Cellular Transition from Quiescence to Proliferation. Cell Rep 20:721-736
Paek, Jaeho; Kalocsay, Marian; Staus, Dean P et al. (2017) Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling. Cell 169:338-349.e11
Boselli, Monica; Lee, Byung-Hoon; Robert, Jessica et al. (2017) An inhibitor of the proteasomal deubiquitinating enzyme USP14 induces tau elimination in cultured neurons. J Biol Chem 292:19209-19225
Susman, Michael W; Karuna, Edith P; Kunz, Ryan C et al. (2017) Kinesin superfamily protein Kif26b links Wnt5a-Ror signaling to the control of cell and tissue behaviors in vertebrates. Elife 6:
Whiteley, Alexandra M; Prado, Miguel A; Peng, Ivan et al. (2017) Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins. Elife 6:

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