Hey, I try to seperate different pyrophosphates via UPLC-MS/MS. For sure, their structure is very similar. For all of them, I measured the same product-ion...Is this a problem? I guess, it isn´t, because I specified different precursor-ions and therefore, there will be a seperation in Q1 of the triple-Quad!?
Best regards
Typically, in MSMS people don't look at just the product ion, but the whole transition. Different transition means different chemical.
It is very typical for all phosphorus-containing chemicals to have same product ions for all chemicals with similar basic structure.
If you have ester groups such as isopropyl and propyl (or any other close structural isomers), the chemicals would typically have exactly same transitions.
If you are interested in identification criteria, you should look at this EU document: http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32002D0657 (click the language version you want)
I assume that you are dealing with isomers. Hence, there is nothing wrong (and acceptable) to detect same precursor ion m/z for various peaks. Try to find out some differences in the MS/MS spectra so that you can acquire some information about the individual structure. If the identity of the fragments are still same, you need to use energy-resolved mass spectrometry (ERMS) for the characterization. ERMS method gives an idea about the stability of various isomers and thus allows the characterization in many cases. plz read our recent article (or many other articles published about ERMS) if you are interested.
Identification of position isomers by energy-resolved mass spectrometry
http://onlinelibrary.wiley.com/doi/10.1002/jms.3607/references
Article Identification of Position Isomers by Energy-Resolved Mass S...
Do they base-line separate in UHPLC or co-elute? First case would be preferred. However, if they co-elute the method is still acceptable since you have different parent ions.
Utilize the chromatographic power to its full extent. It does not matter if the tandem MS is similar. You could reason that the compounds were separated based on their physico-chemical properties. It was not clear from the question whether you are dealing with isomers or not. Chromatographic separation of isomers pose some unique challenges.
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