This proposal requests funds for a high accuracy quadrupole time-of-flight (QTOF) mass spectrometer with high resolution, high sensitivity and fast duty cycle to assist a productive group of investigators at Johns Hopkins University School of Medicine and School of Public Health along with their collaborators in their proteomic studies. This instrument will mainly be used for qualitative studies such as protein identification and analysis of certain post-translational modifications (PTMs) and quantitative studies for measurement of relative abundance of proteins and PTMs. Two existing QTOF instruments (one in the proteomics core facility and one in the Pandey laboratory) are being retired at Johns Hopkins in 2009 as they are old instruments (10 and 7 years old, respectively) and lack many of the advanced features of newer instruments such as fast duty cycles, high mass accuracy, large dynamic range and accurate quantitation capabilities. Owing to this lack of availability of a high resolution tandem mass spectrometer for routine LC-MS/MS type analyses for protein identification and quantitation, the proposed QTOF mass spectrometer is expected to become a major workhorse for the projects in which a team of expert mass spectrometrists and biologists will be greatly benefited. The research groups from the laboratories of Gerald Hart, Philip Cole, Robert Cotter, Bert Vogelstein, Gregg Semenza, Curt Civin, Harold Varmus and Thomas Kensler will be among the major users. Personnel from Akhilesh Pandey's laboratory, along with personnel from Cotter and Hart laboratories, will provide expertise in design of mass spectrometry experiments and LC-MS/MS analysis for those major and other users who do not have mass spectrometry expertise. The advanced features of the QTOF mass spectrometer will be used for iTRAQ and SILAC-based mass spectrometric analysis, among other uses. These quantitative techniques have become very popular and have increased our knowledge about the dynamic changes in proteomes. The biological questions that will be addressed using this mass spectrometry will range from discovery of biomarkers for early detection of cancers and identification of components of protein complexes to studying effects of anti-cancer compounds. Finally, the output of some of the experiments carried out using the proposed QTOF mass spectrometer will be helpful for designing validation experiments using targeted proteomics (e.g. multiple reaction monitoring) on other types of instruments such as triple quadrupole mass spectrometers.

Public Health Relevance

QTOF mass spectrometer is a high resolution mass spectrometer with high sensitivity that allows robust analysis of proteins, peptides and post-translational modifications. It can be used in several modes of operation including data dependent acquisition;parent ion and neutral loss scan modes. This instrument will be essential for the discovery phase and provide essential information about the peptide and proteins to a group of productive biomedical investigators at Johns Hopkins University and their collaborators.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
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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Johns Hopkins University
Schools of Medicine
United States
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Chaerkady, Raghothama; Letzen, Brian; Renuse, Santosh et al. (2011) Quantitative temporal proteomic analysis of human embryonic stem cell differentiation into oligodendrocyte progenitor cells. Proteomics 11:4007-20