Proteomics Instrumentation

Thermo mass spectrometer

Two Thermo Orbitrap Fusion hybrid mass spectrometers with quadrupole, linear ion trap and orbitrap detectors for use with LC-MS, LC-MS/MS, and intact protein analysis. Ultimate 3000 RSLCnano UPLC for nanoflow ultra high pressure liquid chromatography. One of the Fusions has ETD fragmentation for fragmentation of labile species. Ultimate 3000 RSLC UPLC for higher flow rates.

Proteomics Software:

Proteome Discoverer 2.2 and 1.4, MASCOT, and X!Tandem database search algorithms Scaffold 4 Q+, Scaffold PTM, and perSpectives data visualization and validation software, Skyline for peptide and protein quantification. Byonic for protein modification analysis.


Protein and peptide MW determination. MS/MS and MSn of peptides with CID/HCD/ETD. Protein identification from gel bands, gel sections, and complex mixtures. Protein quantitation from spectral counting, stable isotope labeling, and intensity based quantitation. PTM analysis and characterization. High resolution intact and top-down protein analysis for sequencing and PTM characterization.

We are participating in the UT System Proteomics Core Facility Network that supports Jennifer Brodbelt’s development of top-down and UVPD methods on a custom Orbitrap Fusion instrument.  Top-down and UVPD analysis are  cutting edge tools for localization of the modification without digestion of the protein.  Please contact Jennifer Brodbelt directly to enquire about doing a top-down analysis.