This shared instrumentation proposal seeks funding for the purchase of an AB Sciex next generation TripleTOF 5600 quadrupole orthogonal time-of-flight mass spectrometer. This mass spectrometer will be part of an integrated nano-2DLC MS/MS system to be completed through independent funds already committed by the Buck Institute for this purpose. In brief, we propose to operate this integrated TripleTOF mass spectrometry system exclusively for the on-line separation and analysis of complex peptide and protein mixtures as part of large group of 12 independent principal investigators from the Buck Institute and 6 external investigators that represent a total of seven institutions or universities. Together, these researches bring together 21 NIH funded grants, all of which have significant needs for state-of-the-art mass spectrometry for various proteomics applications that require the highest sampling efficiency, resolution and sensitivity. The most critical features of this new instrumentation will be to the high resolution capabilities of data acquisition in both MS1 (40,000) and MS2 (15,000 - 35,000), the number of tandem mass spectra that can be acquired in a given time (typically 35 scans /sec), the exquisite sensitivity (low attomoles) and high dynamic range. These operating parameters will also allow several unique data acquisition scans, including SWATH and pseudo-MRM, and novel quantitation approaches that uses both MS1 and MS2 ion intensity data. The unique capabilities of this instrumentation will be directed at a diverse array of protein and proteomic application where mass spectrometry is used for identification, discovery, and global quantitation in very complex biological samples. The identification and quantitation of biologically important enzymatic and non-enzymatic posttranslational modifications will be a critical use of this new mass spectrometer, including protein phosphorylation, lysine-acetylation, and oxidative damage, among others. Overall, the acquisition of this instrument to the Chemistry &Mass Spectrometry Core at the Buck Institute for Research on Aging will greatly improve the throughput, experimental design, and discovery rate of over 19 projects that are examining key issues of human health and health span, including the biology of aging, neurodegenerative disease, diabetes, cancer, disease biomarker discovery, and infectious diseases.

Public Health Relevance

of this new instrumentation to human health is significant with over 19 independent researchers at seven institutions that will use this new technology to improve their ongoing studies in the basic biology of aging and age-related diseases, including Huntington, Alzheimer and Parkinson's disease, breast cancer, and diabetes. In addition, a group of external collaborators at University of Iowa will participate in studies on microbial pathogens that cause respiratory disease, tularemia, and otitis media, and second group at the Gladstone Institute and Joslin Diabetes Center on metabolic syndrome and diabetes.

National Institute of Health (NIH)
Office of The Director, National Institutes of Health (OD)
Biomedical Research Support Shared Instrumentation Grants (S10)
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Special Emphasis Panel (ZRG1-BCMB-D (30))
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Birken, Steven
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Buck Institute for Age Research
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Basisty, Nathan; Meyer, Jesse G; Wei, Lei et al. (2018) Simultaneous Quantification of the Acetylome and Succinylome by 'One-Pot' Affinity Enrichment. Proteomics 18:e1800123
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
Schilling, Birgit; Gibson, Bradford W; Hunter, Christie L (2017) Generation of High-Quality SWATH®Acquisition Data for Label-free Quantitative Proteomics Studies Using TripleTOF®Mass Spectrometers. Methods Mol Biol 1550:223-233
Post, Deborah M B; Slütter, Bram; Schilling, Birgit et al. (2017) Characterization of Inner and Outer Membrane Proteins from Francisella tularensis Strains LVS and Schu S4 and Identification of Potential Subunit Vaccine Candidates. MBio 8:
Meyer, Jesse G; Schilling, Birgit (2017) Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques. Expert Rev Proteomics 14:419-429
Bullard, Steven A; Seo, Seongjin; Schilling, Birgit et al. (2016) Gadd45a Protein Promotes Skeletal Muscle Atrophy by Forming a Complex with the Protein Kinase MEKK4. J Biol Chem 291:17496-17509
Meyer, Jesse G; D'Souza, Alexandria K; Sorensen, Dylan J et al. (2016) Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH). J Am Soc Mass Spectrom 27:1758-1771
Mark, Karla A; Dumas, Kathleen J; Bhaumik, Dipa et al. (2016) Vitamin D Promotes Protein Homeostasis and Longevity via the Stress Response Pathway Genes skn-1, ire-1, and xbp-1. Cell Rep 17:1227-1237
Schilling, Birgit; MacLean, Brendan; Held, Jason M et al. (2015) Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows. Anal Chem 87:10222-9
Schilling, Birgit; Christensen, David; Davis, Robert et al. (2015) Protein acetylation dynamics in response to carbon overflow in Escherichia coli. Mol Microbiol 98:847-63

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