Skip to Content


What quantity of sample do I need to submit?

0.5 milligram is usually sufficient for multiple runs by direct probe EI /CI. This may seem like a lot of material, but direct probe EI / CI is not as sensitive as other techniques such as Electrospray. The exception to the 0.5 milligram guideline is in the case of very small, highly volatile compounds, with boiling points below 100 C. In this case, several milligrams would be preferable, since this type of molecule will evaporate quickly under the high vacuum conditions found inside of the mass spectrometer. We will often freeze such samples in liquid nitrogen prior to inserting them into the spectrometer, so that they will not evaporate as quickly. Samples submitted for electrospray can contain much less material. 50 micrograms would be an ample amount for electrospray. However, we need to know approximately how much sample is present in the vial, so that we do not over dilute or under dilute the sample solution.

In what form should my sample be submitted?

Please submit your samples in neat form, in a small, clearly labeled vial.

What is the procedure for submitting samples?

Please fill out a Mass Spectrum Request Form for each sample. These blank forms can be found in the box outside of room 3411 Chemistry. Or, you can print out the blank form found on this web-site, and fill out the information requested. The more information that you can provide about your samples, the better. You can then place the forms and the samples in the box on the wall outside of room 3411, or you can also hand deliver the samples to us if you have questions or want to provide special instructions. We will place your forms into the queue, and do them as quickly as possible. We will e-mail the results to you. Remaining chemical samples can be retrieved from the boxes on the lab bench in room 3411.

How long does it take to get the results?

Generally within 2-3 days, although this can vary depending upon the sample load, instrument problems, vacation schedules, etc.

I asked for an Exact mass, but only received a nominal mass spectrum.

We always run a nominal mass, full mass range scan on all samples first. If the nominal mass spectrum does not show the expected molecular ion, we cannot do an exact mass.

What is the difference between chemical mass and exact mass?

Chemists often use the chemical atomic masses that are found on the periodic table. These atomic masses represent a weighted average of all of the naturally occurring isotopes of an element. Chemical atomic masses are not correct to use for mass spectrometry of small molecules (under 2000 Da), in cases where you have at least unit mass resolution. In this instance, you must instead use the exact masses of the most abundant individual isotopes, since the mass spectrometer will separate molecules that have different isotopic compositions. For example, carbon has a chemical atomic mass of 12.0110, but the correct value to use for small molecule mass spectrometry would be the mass of carbon-12, which is 12.0000. As another example, the chemical atomic mass of chlorine is 35.4527, but the correct value to use for small molecule mass spectrometry is the mass of chlorine-35, which is 34.9688. On the other hand, when doing mass spectrometry of large molecules, such as large peptides or proteins by MALDI-TOF, the individual isotopic peaks are not resolved. In this case, the chemical or average atomic masses are the better values to use.

What kind of adducts are commonly observed in mass spectrometry?

By CI with ammonia, you will see either an [M + H]+ ion, or an [M + NH4]+ ion, or both, depending on the structure of your molecule. If your compound readily loses water, you might see an [M + NH4 – H2O]+ ion by CI ammonia, which would appear to be a molecular ion, but it is not. It just has the same nominal mass by coincidence. By CI with methane, you will usually observe an [M + H]+ ion, but many compounds also exhibit a significant [M - H]+ ion. By CI with methane you will also sometimes observe much smaller [M + C2H5]+ and [M + C3H5]+ adduct ions. When doing Electrospray on neutral organic molecules, we will often dope the sample with NaCl, and will then see a significant [M + Na]+ ion, although you will sometimes see an [M + H]+ ion as well. By Electrospray, you will sometimes see solvent adducts, such as an [M + Na + MeOH]+ ion. Small molecules tend to cluster when run by Electrospray, particularly if the sample concentration is high.

What ionization and sample introduction techniques are best in my compound?

Stable organic molecules that can go into the vapor phase under vacuum and mild heating will work by EI. Small molecules that do not produce a molecular ion by EI will often display good adduct ions by CI with ammonia. We can generally do exact mass Electrospray on organic compounds whose molecular weight ranges from 300 daltons to 1500 daltons. We would also do Electrospray on samples that are ionic, such as certain organo-metallic compounds. Compounds containing phosphate groups generally run well by negative ion Electrospray. Proteins and peptides can be run by either Electrospray or MALDI.

Can you work with very airy, sensitive samples?

Yes, we introduce samples that are very oxygen or moisture sensitive using a special apparatus.

What are all those "extra" peaks we see in an exact mass spectrum?

In order to obtain an accurate exact mass measurement, we must introduce known reference compounds simultaneously along with the sample. The "extra" peaks are from those reference compounds.