structure elucidation using LC/MS

[moonchips]

Greetings,

We are trying to identify drug product degradants. The only LC/MS we have is one with single quad. I understand we can not have structure elucidation done using single quad, and I only need to get the molecular ion mass.

I am a new user of LC/MS, and I would like to ask some questions:
1. How to confirm it is molecular ion using single quad
2. If I need to run negative ESI mode, do I use essentially the same tune parameters except ESI mode?
3. if I can get molecular ion under a certain condition (cone voltage etc.), can I assume under the same condition, I can get molecular ion for related compounds with similar structures? (say degradants?)
4. for ESI possitive mode, we use 42 to monitor tune file to get a sense of ionization intesity, what about ESi negative mode, and I use the acid to monitor ionization intestity?
5. Does ESI negative mode usually give lower intensity than possitive mode?


Thank you very much.

[sassman]

1. If you know something about what degradates you are expecting to find and you find one, then you can be reasonably sure that you have the molecular ion. However, I don't think you can be absolutely sure. Is it possible on your instrument to change source parameters so that you can get some in source fragmentation to break apart adducts? What instrument are you using?
2. Tune the MS while infusing your compound. Parameters may be very different or may be the same.
3. Sometimes this is true, but many times a different functional group can cause very different behavior.
4. ???
5. Yes.

Instrument conditions can certainly affect adduct formation or ionization state, but mobile phase conditions are probably more important. Try to use the purest solvents and reagents that you can afford for your mobile phase. Trying different pH and pH modifier will also affect adduct formation and ionization.

[orcicdejan]

1. Well, if you're using ESI and have (usually unwanted) adducts, it's easy: just look for [M+H]+, [M+NH4]+, [M+K]+, [2M+H]+, [2M+Na]+... in positive mode, [M-H]-, [M+Cl]-, [M+HCOO]-... in negative (actually, look for mass differences - i.e. 22 for difference between protonated and 'sodiumated', 16 for difference between 'potassiumated' and 'sodiumated'). Probably you won't see all of them. Not a perfect way, and you may need to adjust your mob. phase and energies, but will give you the needed information.

2. If you're asking whether you just switch polarity, and use the tune you used for positive mode, then no. You need to do separate tune for negative mode.

3. Depends on your luck. You should analyze some samples containing those degradants while varying voltages etc, and compare results.

4. I would say, depends on compound structure and experimental conditions. Some cmpds won't give signal in one mode while giving a huge peak in the other. But for acidic compounds (phenolics, carboxylic acids) it will usually give stronger signal (while noise will be lower -> much better S/N ratio). However, if you want to do some fragmentation, it will require much higher energies.