Frequently Asked Questions:

At first, it did not really appear to me that I should have this paragraph included in this web site. But after thinking about it for a little while, I said to myself this could be the most informative entry of all. In my job, students and others ask questions almost daily. Although, I know some of the questions at the present time, I am going to include them as they come along. Theses questions come from all levels. Some from students who never even heard about mass spectrometry. Some are somewhat informed, although via regular classes. Others are fairly informed but they are just missing some. A good number of those latest questions make me think and search for answers. At the present time, I am going to layout those questions as they occur or as they are given to me. The questions will be shown in bold and starting with the Q:, while the answers will be in plain and start with the A:.

Q: I have a sample and I want to do mass spec. What should I do?

A: Just for short, my answer will be: what kind of compound(s) are you expecting? Is it a mixture? do you know some of the chemical and physical properties of your sample? or maybe how did you obtain this sample? If your sample contains organic, non thermolabile, then we should try EI and/or CI.

Q: How high do you heat the sample when doing mass spec?

A: Obviously we are talking solids probe EI or CI. The probe temperature could be heated up to about 500 degree Celsius.

Q: I have a sample, I was told to do CI but I don't know why. Why not EI?

A: In practice, we generally use EI prior to using CI. These two techniques are complementary and not competitive. Let me be clear; When doing EI we are hoping to observe the molecular ion peak. If we don't, well then, perhaps it is decomposed in the gas phase due to the excess internal energy of the ion. In this case, CI with CH4 or NH3 gases is warranted. In the positive ion mode CH4 we are looking usually at MH+, while for NH3 we are expecting MH+ and /or MNH4+. So to answer your question, EI and CI are complementary and EI is usually used before CI especially for unknowns.

Q: My sample seems to not go through the GC, what is your suggestion?

A: Well if you are doing everything right, then perhaps your sample contains thermolabile compounds. If this is the case, we have to try to do ESI. Perhaps try a direct infusion or loop injection first. If we see some relevant peaks, then we can consider to do online HPLC/ESIMS. Another technique to consider is APCI, if your sample work with the APCI, online LC/APCI will maybe be better. I will tell why when we get there.

Q: I want to do ESI but my sample is not soluble in anything. What do you suggest?

A: First, solubility, even if it's poor, is required for doing ESI. Samples maybe poorly soluble, but nonetheless, some of the molecules are trapped in the solvent. So, let's try. Solubility is relative...

Q: I heard from some sources that for ESI we have to use only methanol/water mixture. But my sample is not soluble in that mixture, but very soluble in methylene chloride. What should I do:

A: That is not true. Any solvent can be used successfully with ESI. The reason you have got that info it is because in the early days of ESI, people were using it mainly for peptides and proteins, and for those type of samples, mixture of methanol/water/1% acetic acid is recommended for positive ion mode ESI.

Q: What kind of samples ESI is used for?

A: ESI covers a large spectrum of samples. From low molecular weight polar compounds to high molecular weight biopolymers such as proteins.

Q: I have gotten the ESI data, but there is a peak at 23 mass units higher than what MW is!!

A: Obviously we are talking positive ion mode; well that is probably a sodium adduct. sometimes potassium adducts are observed too at 39 uma higher. In fact, in some cases we spike the sample with some sodium to promote the formation of MNa+.

Q: But my sample doesn't contain sodium. How did it get there?

A: First, sodium, in small quantities, is everywhere. Sometimes, even when we use deionized water, or high grade solvents, we may still see the sodium adduct. If the affinity for the sodium is high, then if there is any out there, it will be in play.

Q: I want to analyze a compound that is present as salt. Is ESI will do?

A: Yes. In general, only the positive ion portion is observed or if doing negative ion mode, only the counter ion (-) will be observed. For example, if you have a sodium salt compound, negative ion mode ESI will yield [M-Na]-

Q: I am writing a publication and I need help with the experimental section of the paper.

A: Click at the following links for that. Those are samples of what is needed for the manuscript. You can, if you need to, make changes accordingly and let me know if you need more help.
ESI
EI
GC/MS
MALDI

Q: I want to analyze a protein with ESI, what is the concentration needed?

A: Of course it depends on the nature of the protein and other factor. Just to tell you a good range: micromolar to less than millimolar solution will be fair.