I usually just calibrate in the 300 to 1800 amu range in Positive Ion mode, and mostly run samples in Positve Ion mode. Sometimes I will double check a result in negative ion mode but get nothing. Sometimes I will get molecular weights which would correspond to a carboxyl adduct of the molecule of interest.
Hi,
Your observations using positive and negative ion mode make sense, considering the fact that ionization can be different/less, or more, efficient for certain compounds, regardless of the ion mode. Peptides, for example, tend to ionize better in the positive ion mode and you'll probably detect [M+nH]n+ ions. In negative ion mode, peptides are usually detected less easily. Other compounds, like sugars, tend to be more easily detected in negative ion mode ([M-nH]n-).
Some compounds form adducts with salt ions that can be detected, such as [M+Na]+ in positive ion mode, or carboxylic adducts in negative ion mode.
Taken together, it greatly depends on the type of molecule you want to analyze what ionization mode is best suited. Calibration of your mode of choice will ensure that you generate accurate mass data, which in many cases is useful.
Hope this helps!
Thank you Eef Dirksen for those insightful comments. I believe most are peptides , however some are experimental medicinal compounds that have functional groups that can affect cell metabolism - especially cancer cells! I get ALOT of M + 2 (presumably doubly protonated) while using positive ion mode. But the (2+) adducts match the MW of compounds of interest (+2). Why wouldnt they occur on an m/z axis at half the expected outcomes? As you mentioned I get ALOT of Na adducts; sometimes they are the best peaks. Those are no problem and lead to successful formula confirmations. I am most puzzled about the 2+ adducts. Is something else (other than double protonation) occurring. Any comments will be appreciated! Thanks again for weighing in.
Clifford Morse, If you wish to know if have [M+2H]+2 you can take a look at the isotopes peaks. If the gap between the isotopes in ~1 amu it is not your compound. but if it is ~0.5 amu it is probably it.
And as Noel W Davies wrote before me, always calibrate your machine.
Hope it was helpful!
Thank you Noel W Davies for weighing in. I am not at liberty to share MWs or spectra as they are medicinal compounds which may soon be undergoing patent approvals, clinical trials, etc... so it is sensitive information.
Your comments about calibrating in same polarity are helpful and true. Thanks again!
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