Chemical and Proteomic Mass Spectrometry Core Facility

We offer a wide range of mass spectrometric services, from basic mass measurement to complex proteome analyses. We encourage investigators to contact the Mass Spec Core regarding their experimental needs, so that we can discuss how to get the best results for you.

Basic mass measurement

Typically done on either the QToF II or the AB Sciex 5800 MALDI TOF-TOF. Your samples will be introduced into the mass spectrometer by direct infusion, and you will receive a mass spectrum either by print-out or by email which shows the mass of the species in the sample. This service is often used to verify the product of synthesis, for example. The expected mass can range from small molecules to medium-size proteins. Samples will need to be approximately 100 µL in volume, with a concentration of 25-50 µM. Pure water is the solvent of choice, but we can also accept solvents such as methanol or acetonitrile. Avoidance of any kind of salts is extremely important, as this will greatly cloud the mass spectrum and may make the species of interest impossible to detect.


Some experiments may require fragmentation of the precursor ion in order to answer the investigator’s questions. We have several instruments capable of fragmentation, so the selection of the instrument will be determined by availability and the requirements of the sample. The sample concentration and purity are the same as needed for basic mass measurement.


LC-MS can be used if a sample has several different species that need separation in order to be properly analyzed, or if a sample has too much salt contamination. The sample concentration can be lower; the typical concentration is 100 fmol of a standard peptide. The volume required is also lower, as no more than 10 µL can be injected on-column. LC-MS can be performed on either the Orbitrap or can be done by spotting a plate and running it on the MALDI TOF-TOF.

Exact mass measurement

Performed either on the QToF II or the Orbitrap. Mass measurement with <10 ppm mass accuracy. Concentration and purity requirements are equivalent to those needed for basic mass measurement.

Protein identification

Can be performed on either the Orbitrap or the MALDI, the instrument will be selected based on the concentration and complexity of the sample. Protein ID samples can be either gel bands or solutions; concentration can range from light silver-stain to dark Coomassie. If silver stain is required, we suggest the silver stain methods listed on our protocols page, as some silver-stain kits have poor recovery for mass spectrometry. We can cut bands from a gel either here at the Mass Spec Core, or investigators can cut their own bands of interest, being careful to minimize keratin contamination. Then the gel bands can simply be placed in Eppendorf tubes and brought to the lab. Analysis involves enzymatic digestion (usually with trypsin, though other enzymes may be considered), analysis with LC-MS/MS, and subsequent software analysis. Investigators will receive a list of their proteins, including the peptides detected, in the form of a Scaffold file. Charges are based on the complexity of the sample, including whether ion exchange fractionation is required

Other services

We encourage investigators to arrange a meeting with the Mass Spec Core staff to discuss their projects. Experiments not listed here, such as elucidation of post-translational modifications or relative quantitation are viable projects for the Mass Spec Core, but may require a longer turnaround time or a higher quantity of sample.

Facility director: 

Kristina T. Nelson