In addition to helping the NHLBI investigators, our research involves developing new approaches for PTM characterization and absolute protein quantitation (e.g. measuring occupancy of nitrosylation with cys-TMT tags, acetylation occupancy, tissue ubiquitination and absolute quantification of a mitochondrial protein panel). The main accomplishments for the Proteomics Core individual research are the following: 1. Acetylation on lysine: We developed the workflows for identification, relative quantification and occupancy measurements (Chen et al, ASMS 2012, poster). Several NHLBI investigators have taken advantage of this research and applied it to e.g. heart tissue (Murphy lab, paper in preparation), identifying RIP1 acetylation (Finkel lab, Nature paper) and liver tissue (Sack lab, EMBO paper). 2. Nitrosylation identification and occupancy measurements: We developed the workflows for identification of nitrosylation sites after SNO-RAC enrichment and worked out the details for occupancy measurements using cys-TMT tags. Dr. Murphys lab utilized these techniques to identify nitrosylation sites in the mouse heart tissue (Kohr et al, Circulation Research, 2011) and to measure occupancy of nitrosylation (Kohr et al, Circulation Research, 2013). 3. Ubiquitination: We are developing ubiquitination and SUMOylation workflows for identification and quantitation. We have applied this technology to analyze heart tissue (Swatkoski et al, ASMS, 2012, oral presentation) 4. Software development: The PCF has improved the software for relative quantification QUOIL to be able to accommodate new types of raw data files. Dr. Wang also developed software for iTRAQ data analysis (QUARI) whose integral part is the ability to correct the iTRAQ ratios based on the isolation purity of precursor ions (Wang et al, ASMS 2012, poster). 5. Absolute protein quantitation: We developed a targeted peptide method taking advantage of the sensitivity of Orbitrap Velos to measure absolute abundance of STAT3 transcription factor in the pig heart tissue (Phillips et al, JBC, 2010). 6. Development of mitochondrial protein panel: We are developing targeted peptide analysis on Velos Elite to simultaneously follow specific mitochondrial proteins in healthy and diseased platelets (working with Drs. Balaban and Sack). 7. Clinical proteomics: Depletion of the most abundant serum proteins to study the protein differences in patients samples (collaboration with Dr. Saligan from NINR). Using saliva as a possible tool for biomarker discovery (collaboration with Dr. Melvin from NIDCR).

Project Start
Project End
Budget Start
Budget End
Support Year
6
Fiscal Year
2013
Total Cost
$1,496,411
Indirect Cost
Name
National Heart, Lung, and Blood Institute
Department
Type
DUNS #
City
State
Country
Zip Code
Wang, Honghui; Drake, Steven K; Yong, Chen et al. (2016) A Novel Peptidomic Approach to Strain Typing of Clinical Acinetobacter baumannii Isolates Using Mass Spectrometry. Clin Chem 62:866-75
Dai, C; Yao, X; Gordon, E M et al. (2016) A CCL24-dependent pathway augments eosinophilic airway inflammation in house dust mite-challenged Cd163(-/-) mice. Mucosal Immunol 9:702-17
Zhang, Yi; Chen, Yong; Gucek, Marjan et al. (2016) The mitochondrial outer membrane protein MDI promotes local protein synthesis and mtDNA replication. EMBO J 35:1045-57
Stoehr, Andrea; Yang, Yanqin; Patel, Sajni et al. (2016) Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes. Cardiovasc Res 110:346-58
Abeykoon, Amila H; Noinaj, Nicholas; Choi, Bok-Eum et al. (2016) Structural Insights into Substrate Recognition and Catalysis in OmpB by Protein Lysine Methyltransferases from Rickettsia. J Biol Chem :
Sun, Junhui; Aponte, Angel M; Menazza, Sara et al. (2016) Additive cardioprotection by pharmacological postconditioning with hydrogen sulfide and nitric oxide donors in mouse heart: S-sulfhydration vs. S-nitrosylation. Cardiovasc Res 110:96-106
Alves, Gelio; Wang, Guanghui; Ogurtsov, Aleksey Y et al. (2016) Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance. J Am Soc Mass Spectrom 27:194-210
Lu, Zhongping; Chen, Yong; Aponte, Angel M et al. (2015) Prolonged fasting identifies heat shock protein 10 as a Sirtuin 3 substrate: elucidating a new mechanism linking mitochondrial protein acetylation to fatty acid oxidation enzyme folding and function. J Biol Chem 290:2466-76
Chung, Youn Wook; Lagranha, Claudia; Chen, Yong et al. (2015) Targeted disruption of PDE3B, but not PDE3A, protects murine heart from ischemia/reperfusion injury. Proc Natl Acad Sci U S A 112:E2253-62
Menazza, Sara; Aponte, Angel; Sun, Junhui et al. (2015) Molecular Signature of Nitroso-Redox Balance in Idiopathic Dilated Cardiomyopathies. J Am Heart Assoc 4:e002251

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