Research

Research
- Proteomics Core Research

We provide access to mass spectrometry and gel based proteomics for identification and quantitation of proteins and their posttranslational modifications (PTM). We have state-of-the-art equipment, including an Orbitrap Fusion instrument.

Our workflows for relative protein quantitation are based on DIGE, label-free, SILAC and TMT approaches. We can also help investigators identify and quantify protein posttranslational modifications, including phosphorylation, nitrosylation, acetylation, ubiquitination, succinylation, etc. We provide training in proper sample preparation and lead the researchers through mass spectrometric analysis to data searching and interpretation. Users have access to a variety of proteomics software platforms (Mascot, Proteome Discoverer, Sequest, Scaffold) for re-searching the data or viewing the results.

In addition to helping the NHLBI investigators, we develop new approaches for PTM characterization and absolute protein quantitation.

We have state-of-the-art equipment, including the following mass spectrometers:

  1. two Thermo Orbitrap Lumos instruments (one with ETD ionization)
  2. Thermo Orbitrap Elite instrument
  3. ABI 5800 MALDI-TOF/TOF

We offer the following types of analyses:

  1. Protein identification (from in-solution, 1D/2D gel)
  2. Relative protein quantitation (label-free, SILAC, TMT, DIGE)
  3. Peptide/protein fractionation using gels, offline basic reversed LC, IEF or SCX
  4. Protein post-translational modifications – identification and relative quantification (phosphorylation, acetylation, succinylation, malonylation, nitrosylation, ubiquitination, nitration, SUMO, sulfhydration)
  5. Serum depletion and protein identification/quantification
  6. We work with investigators on custom projects (either targeted proteins or systems biology approaches)

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).

Selected Publications

A CCL24-dependent pathway augments eosinophilic airway inflammation in house dust mite-challenged Cd163(-/-) mice.

Authors: Dai C, Yao X, Gordon EM, Barochia A, Cuento RA, Kaler M, Meyer KS, Keeran KJ, Nugent GZ, Jeffries KR, Qu X, Yu ZX, Aponte A, Gucek M, Dagur PK, McCoy JP, Levine SJ
Mucosal Immunol 2016 May 01;9(3):702-17

Cyclophilin D modulates mitochondrial acetylome.

Authors: Nguyen TT, Wong R, Menazza S, Sun J, Chen Y, Wang G, Gucek M, Steenbergen C, Sack MN, Murphy E
Circ Res 2013 Dec 06;113(12):1308-19

Essential role of nitric oxide in acute ischemic preconditioning: S-nitros(yl)ation versus sGC/cGMP/PKG signaling?

Authors: Sun J, Aponte AM, Kohr MJ, Tong G, Steenbergen C, Murphy E
Free radical biology & medicine 2013 Jan 01;54:105-12

Global analysis of neuronal phosphoproteome regulation by chondroitin sulfate proteoglycans.

Authors: Yu P, Pisitkun T, Wang G, Wang R, Katagiri Y, Gucek M, Knepper MA, Geller HM
PloS one 2013 Jan 01;8(3):e59285