Protein Identification from less complex samples

We analyze proteins from gel bands/spots and in solutions, eg. pure proteins/IPs/cell lyates/tissue lysates.

Analysis of full length proteins

We have the capability to perform intact protein analysis by MALDI. However, the outcome of this type of experiment is dependent on the protein, the size of the protein and the purity of the sample.

Global protein expression profiling (shotgun proteomics)

  1. Label-free quantification: Each sample is analyzed individually with MudPIT (2D LC-MS/MS). Spectral counting method (other methods under developing) is used to generate relative quantification for proteins in different samples.
  2. Labeling-based quantification: We utilize currently available labeling strategy such as the stable-isotope based labeling strategy (e.g. SILAC and 15N SILAM) and isobaric mass tags labeling (e.g. iTRAQ and TMT). Please consult the center directors for experimental design.

Identification of post-translational modifications

For these types of experiments, we will digest your sample with different proteases to get good sequence coverage of the target proteins and use different analysis strategies and software to identify the desired modification. We also perform large-scale PTM analyses such as phosphorylation, ubiquitination, oxidation, acetylation, etc. Manual inspection and analysis will be performed to provide publication quality spectra for manuscripts.

De-novo sequencing of monoclonal antibodies

In collaboration with N.Bandeira (UCSD), we are able perform complete de-novo sequencing of monoclonal antibodies (Nat.Biotech, 2008, 26:1336-1338).

Analysis of small molecules

If you are interested in the accurate mass of a small molecule (drug/DNA fragment/peptide), we have the capability to give you <5ppm accuracy on our Orbitrap.


If you are interested in pharmacokinetics, please contact the Translational Experimental Therapeutics Laboratory.