Proteomics Analysis

Comprehensive gel-based proteomic services:
  1. Protein identification by liquid chromatography-Mass Spectrometry/ Mass Spectrometry (LC-MS/MS)
  2. Mass spectrometry (MS) database searches including post-translational modification (i.e., phosphorylation, oxidation) searches
  3. Gel-free proteomics with isobaric mass tagging (TMT, iTRAQ, SILAC)
  4. De novo peptide sequencing (PEAKS software)
  5. Protein separation by high resolution 2D electrophoresis
  6. Differential proteomic analysis (gel image analysis)
  7. Consulting for in silico prediction of protein structure - potential drug design, binding pockets, etc. 

Gel-based Proteomics

We routinely perform:

  • Tryptic digestion of targeted proteins, nanospray LC-MS/MS of the tryptic peptide mixture and database searches for protein identification
  • High resolution 2D gel electrophoresis to separate complex biological samples
  • Quantitative gel image analysis for targeting of differentially expressed proteins


Nanospray LC technology allows us to perform proteomic analysis at subpicomolar levels.  A Coomassie blue-stained protein will typically yield high quality protein identification results.  We provide a full report ( see an example ) on every protein identified in your sample. The following link is  an actual example of our typical gel-based proteomic analysis.  

In addition, for a small fee (Fee Schedule), we provide a standard .mgf and/or .mzML file of your raw LC-MS/MS data that allows you to search on your own using OMSSA or X!tandem.  Both are open and free search engines available from SearchGUI or the Trans Proteomic Pipeline (TPP).  Learn how to perform your own searches by following the either group's instructions and tutorials.  We have included a more detailed tutorial for the TPP in our Protocols page. 

Post-translational modifications

Along with protein identification, we provide an additional search for post-translational modifications (PTMs). At your request, various PTMs (phosphorylation, oxidation, alkylation, etc.) linked to certain amino acid residues can be included in the database search. If possible, the modified protein sample should be compared to the unmodified protein in order to validate the PTM search. We always include oxidized methionine and iodoacetamide alkylated cysteine in all our database searches.