This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.Technology Core Projects 3: Quantitative mass spectrometry of protein modifications and detecting protein modifications in complex mixtures - Akhilesh Pandey, Assistant Professor, Dept. of Biological Chemistry and IGM.
The aim i s to develop quantitative methods for mapping/detecting sites of acetylation, methylation, ubiquitylation and SUMOylation in proteins. In addition, his methods can be routinely applied to protein mixtures by prefractionation (MUDPIT) methodologies. Dr. Pandey also heads a major effort in protein bioinformatics.This involves a critical databasing effort with the Institute of Bioinformatics in Bangalore, India.1. To develop stable isotope labeling in cell culture (SILAC) method to obtain quantitative information at the protein and peptide level from multiple samples (up to four different states) in a single experiment. This will allow for simultaneous relative quantitation of i) protein abundance in all 4 states, and, ii) post-translational modifications in all 4 states.2. To develop mass spectrometric methods for improved detection of acetylated, methylated and ubiquitylated peptides. We will develop precursor ion scanning as well as neutral loss scanning methods to selectively identify peptides carrying an acetyl, methyl or ubiquitin moieties from complex mixtures.3. To develop software tools for analysis of quantitation and to create a repository of all lysine modifications in yeast and humans. To generate pathways involving lysine modifications in a standardized format and to generate mapping of PTMs on the protein sequences in XML file format to enable better searching of protein databases using mass spectrometry-derive

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54RR020839-04
Application #
7622841
Study Section
Special Emphasis Panel (ZRG1-BST-D (55))
Project Start
2007-08-01
Project End
2008-07-31
Budget Start
2007-08-01
Budget End
2008-07-31
Support Year
4
Fiscal Year
2007
Total Cost
$368,310
Indirect Cost
Name
Johns Hopkins University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21218
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Cox, Eric; Hwang, Woochang; Uzoma, Ijeoma et al. (2017) Global Analysis of SUMO-Binding Proteins Identifies SUMOylation as a Key Regulator of the INO80 Chromatin Remodeling Complex. Mol Cell Proteomics 16:812-823
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Zhong, Jun; Martinez, Marissa; Sengupta, Srona et al. (2015) Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O-GlcNAc in the DNA damage response pathway. Proteomics 15:591-607

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