I'm trying to do compound optimization for acetic acid on a EI-MS. Later on it would be also run via HPLC to the MS. But I do only get fragments of 53/54 and 32. Also I need a high concentration to be able to do a compound optimization for the 32 fragment (...around 1mM solution).

I looked up other mass spectra of acetic acid online.... and they got nice fragments around 43/45 and 29

...what am I doing wrong?

Edit: for clarification of the question

  • We work with ESI, also tried it with APCI
  • Acetic acid as a liquid, with mobile phase of water and formic acid
  • yes, it is acetic acid
  • in the meantime we did a blank (thanks for the suggestion!) and we also got the 32 fragment... but non at 60/61 (for positiv mode) so it should actually work, if we first make Q1 for 61 and then look for fragments
  • we re-run a fresh dilution with UV-water ... and got some nicer fragments... but unstable turbo spray signal.
  • $\begingroup$ Are you using a solvent? If so, what is it? $\endgroup$ – Ben Norris Dec 7 '13 at 0:01
  • $\begingroup$ I'd expect fragments with m=60 (M), 45 (M-15) and 43 (M-17) - just like you ;) For m=54, i can imagine C4H6 from the retro-Diels-Alder reaction of cyclohexene. $\endgroup$ – Klaus-Dieter Warzecha Jan 10 '14 at 19:27

I ran this question past our mass spec. guy, and he offers the following suggestions:

  • Have you run a blank to ensure you are not just measuring some other random compound; Or contaminants from the instrument; Or gas system.
  • Be aware when measuring ions less than 45m/z that you are not just measuring ions from air leaking in. For example: 18/19 is H2O; 28 is N2; 32 is O2; 40 is Ar; 44 is CO2. There are probably other ions to watch as well.
  • Is the ionization energy set to 70eV and it is measured in positive ion mode as that is what most online libraries use
  • Is too much sample being injected in the instrument as you do measure different fragment patterns when a lot of sample is injected as the molecular ion may be a charge bound cluster (similar to what is seen in ESI).
  • Is the acetic acid reacting with anything in the sample introduction path which is giving another compound? If it is a water injection into a GCMS, not only are you destroying your column but the solvent will expand in the injection port and goes back into your gas system as water has a very high expansion when going from liquid to gas.
  • Are you sure, really, really sure you are using acetic acid and not something else?
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