I have isolated several compounds recently and tried to measure their molecular weight or m/z values using LC/MS instrument in order to elucidate their chemical structures. However, I found that all of these compounds ionized well in the positive scan mode, but they did not ionize well in the negative mode where the molecular ion peak could not be observed. Instead, the ionization was relatively unfavorable where many ion peaks were observed with no clear indication of the desired molecular peak. I would like to figure out the reason behind this.
I would greatly appreciate if members of RG and professionals could give me some suggestions or advice about my doubt.
Thanks in advance!
That what it is supposed to be..Basic compound will have positive charge, say in water. So you will observe it in pos mode normally. Acid compound will have neg charge and run well in neg. You cannot force to be the opposite. Like most of the guys will like girls and girls will like guys not girls. Of course some compounds can exhibit pos or neg depending on the pH, so you can run both.
It is often observed that one mode in mass spec works better than the other, and as Narong says, it has to do with the facility of forming positive or negative ions for the compound type you have encountered.
You say your compound ionized well in positive mode, but not in negative. Does your compound contain basic nitrogen? If so, then it may be difficult to get negative ionization. But if it is a neutral compound or contains carboxylic acids, then it is often possible to get both positive and negative ionization. For example if you have formate or formic acid in the solution then you may well get both formate adducts in negative mode and protonated (or sodium or ammonium adducts etc.) ions in positive.
A word of caution. Always remember that any compound isolated could happen to be poorly ionizable, but contaminated by traces of something that ionizes easily, and that could lead one to draw the wrong conclusion about the molecular weight. Also you could have an ion that is an adduct (e.g. with Na+ or NH4+), or your molecule might fragment easily during ionization (e.g. loss of CO2 or H2O).
It depends on which group of your compound. Compounds with carboxylic and polyhydrxoylic groups should be analyzed with negative mode
Yes i also agreed with above mentioned suggestions. Moreover you can try APCI ionization method (I am not clear about your ionization methods).
Generally basic compounds with NH2 get ionized in positive mode while acidic compounds with COOH group get ionized easily in the negative mode of ionization.
This is because in positive mode of ionization proton gets added while in negative mode of ionization proton gets removed.
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