Core A The DDBTRCC Proteomics Core A is coupled to the Johns Hopkins University (JHU) School of Medicine Mass Spectrometry and Proteomics Facility and provides DDBTRC Center investigators faster access to the services of the JHU Core, a designated Core Proteomics Specialist with whom to work, a specific biostatistician/bioinformatician for post identification/quantification data analysis, all at a reduced cost. The Proteomics Core uses mass spectrometry coupled to multi-dimensional separations by column chromatography or gel electrophoresis to identify, quantify or characterize proteins and their post-translational modifications, expressed in well characterized protein fractions from cells, tissues or body fluids. Techniques such as isobaric mass tag labeling (TMT, tandem mass tags, or iTRAQ, isobaric tag for relative and absolute quantitation) and stable isotope labeling of amino acids in cell culture (SILAC), as well as non-labeling methods (MuDPIT, multi-dimensional protein identification technology) are available for quantifying relative differences in protein expression and post-translational modifications, such as acetylation, AMPylation, citrullination, glycosylation, phosphorylation, nitrosation, proline hydroxylation, ubiquitination and novel cleavage sites. For determining the amount of specific proteins, the Core offers recently established targeted proteomic methods, such as Absolute Quantification (AQUA) and Protein Standard Absolute Quantification (PSAQ) methods. In addition, the Core offers high resolution mass and fragmentation analysis of intact proteins, a top down approach to characterize proteins and their modifications. All Core services include pre- and post-analysis consultation on sample preparation; a Core Proteomic Specialist assigned to receive and analyze the samples; proteolytic digestion, peptide extraction, labeling and fractionation; nano-liquid chromatography separation coupled to tandem mass spectrometry analysis; database searching, data analysis and interpretation, compiled results reports; and educational programs through core presentations and technical workshops. A biostatician/bioinformatician is available when more in depth statistical and ontological analyses of the proteomic results is needed. For DDBTRCC investigators who wish to perform their own analysis the Core provides access to proprietary software and equipment, and Core workshops are offered several times a year on operating the Core MALDI mass spectrometer. 18 current Members, 6 Associate Members and a total of 30 Core Center investigators from our entire funding period have used the Proteomics Core and 51 manuscripts are attributed to this Core.

Public Health Relevance

Proteomics Core A The Proteomics Core which is part of the JHU Mass Spectrometry Core, uses mass spectrometry to not only identify and quantify proteins of interest to Core Center investigators, but also identifies and quantifies the protein modifications and the proteins with which they interact and by which they are regulated. Core Center investigators get faster access, reduced cost and are assigned a designated Core Proteomics Specialist and biostatistician/bioinformatician.

Agency
National Institute of Health (NIH)
Institute
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Type
Center Core Grants (P30)
Project #
5P30DK089502-10
Application #
9951048
Study Section
Special Emphasis Panel (ZDK1)
Project Start
Project End
Budget Start
2020-06-01
Budget End
2021-05-31
Support Year
10
Fiscal Year
2020
Total Cost
Indirect Cost
Name
Johns Hopkins University
Department
Type
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21205
Avula, Leela Rani; Chen, Tiane; Kovbasnjuk, Olga et al. (2018) Both NHERF3 and NHERF2 are necessary for multiple aspects of acute regulation of NHE3 by elevated Ca2+, cGMP, and lysophosphatidic acid. Am J Physiol Gastrointest Liver Physiol 314:G81-G90
Moinova, Helen R; LaFramboise, Thomas; Lutterbaugh, James D et al. (2018) Identifying DNA methylation biomarkers for non-endoscopic detection of Barrett's esophagus. Sci Transl Med 10:
Liu, Xi; Abraham, John M; Cheng, Yulan et al. (2018) Synthetic Circular RNA Functions as a miR-21 Sponge to Suppress Gastric Carcinoma Cell Proliferation. Mol Ther Nucleic Acids 13:312-321
Liu, Xi; Cheng, Yulan; Abraham, John M et al. (2018) Modeling Wnt signaling by CRISPR-Cas9 genome editing recapitulates neoplasia in human Barrett epithelial organoids. Cancer Lett 436:109-118
Dejea, Christine M; Fathi, Payam; Craig, John M et al. (2018) Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science 359:592-597
Aberle, M R; Burkhart, R A; Tiriac, H et al. (2018) Patient-derived organoid models help define personalized management of gastrointestinal cancer. Br J Surg 105:e48-e60
Singh, Varsha; Yang, Jianbo; Yin, Jianyi et al. (2018) Cholera toxin inhibits SNX27-retromer-mediated delivery of cargo proteins to the plasma membrane. J Cell Sci 131:
Chung, Liam; Thiele Orberg, Erik; Geis, Abby L et al. (2018) Bacteroides fragilis Toxin Coordinates a Pro-carcinogenic Inflammatory Cascade via Targeting of Colonic Epithelial Cells. Cell Host Microbe 23:203-214.e5
Liu, Liansheng; Zhu, Yaohui; Noë, Michaël et al. (2018) Neuronal Transforming Growth Factor beta Signaling via SMAD3 Contributes to Pain in Animal Models of Chronic Pancreatitis. Gastroenterology 154:2252-2265.e2
Nakamura, Hideki; Lee, Albert A; Afshar, Ali Sobhi et al. (2018) Intracellular production of hydrogels and synthetic RNA granules by multivalent molecular interactions. Nat Mater 17:79-89

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