Chromatography Forum

Hi All,

I've some MSMS data (MGF files) for which I've found that there is a fragment mass almost equal to the mass of the precursor ion with highest abundance among the msms peaks, and some masses greater than the precursor. Is this something uncommon suggesting that the precursor is not adequately fragmented and formed adduct masses larger than the precursor?

Secondly, for the mass 457.5577859, can it result due to a loss of water molecule?

I'm enclosing part of the ms2 spectra with fragments sorted by their abundances. The third colums shows the relative abundance compared to the most abundant ms2 peak.

caveat: peptides aren't my thing
(1) the precursor mass appearing as the major fragment isn't uncommon, and can indicate that there wasn't enough collision energy
(2) in your case, the major fragment is actually an isotope peak of the precursor mass, not the actual precursor?? If it's not the most abundant isotope peak, then it's worth taking a look at how it happened, which might depend on your instrument. Some instruments (e.g. ion traps) can apply fragmentation energy to a particular bandwidth of masses, which may not be the same bandwidth as was selected for MS2, so it's possible to collect, say, 3 isotope peaks, but fragment only two of them efficiently. Also, if you're really unlucky, in any instrument, you can find a contaminant with nearly the same mass as the expected product, but which is much tougher and won't fragment. In this scenario your expected product fragments, leaving a near-isobaric peak from the unfragmented contaminant. I don't think this has happened in your case.
(3) It's quite normal to get fragments "bigger" than the precursor when working with multiply charged ions, because you can lose charge as well as mass. The mass:charge ratio of a singly-charged fragment from your triply-charged precursor could reach nearly three times the value of the precursor (i.e. your original precursor has a mass of 463 * 3 = 1389, so if you lose two charges and a bit of mass, you could theoretically get a singly charged fragment showing up at over 1300!).
(4) yes, a loss of 6 from a triply-charged ion could well indicate a loss of 18, water. But because you're looking at a peptide, a loss of 17 (ammonia) is also likely. You need to check which isotope peak you're looking at, to make sure the loss is really 6 and not 5.67; it's very easy to end up looking at the mass difference between different isotope peaks of a precursor ion and a fragment when there are multiple peaks with good intensity.

Thanks a ton