CMS Services

Protein Identification

Protein identification is most commonly accomplished by proteolytic digestion followed by MS analysis. Sample are typically submitted as gel bands, pelleted pure proteins, or proteins in solution without detergents or glycerol (preferably in 25mM Ammonium Bicarbonate buffer, pH=7-8). Samples are enzymatically digested, typically with mass spec grade trypsin, and analyzed by either MALDI-TOF-MS/MS or nano-capillary HPLC/MSMS. The resulting MS and MS/MS data can then be queried against a specific database for peptide and protein identification.

Exact Mass Analysis for Proteins

Clients often need to know the exact mass of a purified protein. Samples need to be in Na and K free buffers, in the absence of detergents, chaotrophic agents, and glycerol. We recommend ammonium acetate or ammonium bicarbonate buffers if they are required.

Intact Protein Complex Mass Determination

Masses of purified protein complexes and subunit composition can also be determined in our facility. This is non-routine work and we highly recommend a consultation before submitting your samples.

Proteomic Analysis

Complex mixtures of proteins can also be identified by MS. However, protein ID requires LCMS for analysis. Prefractionation of the proteins, such as 1D SDS-PAGE can be used to increase the numbers of proteins identified by the experiment. Other approaches include separation of digest proteins peptides using high pH LC, collecting fractions and running those fractions by low pH LCMS. Yet another approach is to run long gradients using normal reverse phase chromatography-MS. Set up a consultation and we can decide which is best for you. We also offer semi-quantitative techniques, either label-free or labeling for your proteomic analysis.

Posttranslational Modification Site Determination

Starting with a single highly purified protein, either as a gel band or purified protein, multiple sites of modification, eg. Glycosylation, phosphorylation, acetylation and others, can be determined. This process is non-routine and typically requires multiple digestion enzymes. We recommend you set up a consultation before beginning this work.