Proteomics Services

Protein identification

Peptide sequencing and protein identification via capillary LC-MSMS measurements and database searches.

This service provides investigators with the ability to identify proteins that are contained in samples such as gel spots or slices, and solutions. The service includes the digestion of the sample prior to the MS/MS measurements, chromatographic separation using UHPLC  that is coupled  to a Thermo Scientific LTQ-Orbitrap XL mass spectrometer. All MS/MS spectra are searched against protein databases using various proteomics software and search engines.

Samples can be submitted for proteomic analysis as gels or in solution. Reduction and alkylation will be conducted prior to the enzymatic digestion.Trypsin is the default enzyme, but by request, a variety of other enzymes (e.g., chymotrypsin, endoproteinase GluC, etc.) may also be used.

At least 1 pmol of protein is necessary for a proteome analysis.


  • Quantitative proteomics

Definition of the relative levels of the proteins in different cell types or the shifts in these levels as a response to treatment


  • PTM identification

            Post-translational modifications are chemical changes to a protein that occur after translation widening the range of functions of the final            protein.The most frequently analyzed modifications are: phosphorylation, oxidation, deamidation, methylation and acetylation.


  • De novo sequencing

Peptide De novo sequencing is the analytical process that derives a peptide amino acid sequence from its tandem mass spectrum (MS/MS) without the assistance of a sequence database.

  • Analysis of protein-protein interactions
  • Global and targeted  quantification of specific PTM
  • Intact protein analysis

Mw determination of intact proteins

  • N terminus identification
  • Sample preparation:

Sample cleanup and enrichment

  • Desalting

The goal of desalting is to remove buffer salts from a sample in exchange for water. Desalting is preformed using ZipTip® pipette tips. It is intended for concentrating and purifying peptide, protein or oligonucleotide samples.

It is mandatory if the sample contains contaminants such as salt

  • PTM (phos) enrichment Fe, Ga-IMAC
  • Chromatography with capillary columns

Small molecules:

  • HRMS

High resolution mass spectrometry is generally used to measure accurate masses (and thereby enable the determination of elemental compositions)


  • Structural analysis of small molecules (MSn)

Structural elucidation by fragmentation and MSn measurements