This is not a homework question, but for research.

I am performing mass spec on serum metabolites using Thermo Q Exactive PLUS with a HESI source which was set to a spray voltage of -2.7kV under negative mode. During the metabolite identification step: I am curious why the mass was used (supplied by my collaborator) differs from the mass I calculated.

Sorry, I am new to chemistry or mass spec: but in the software, we can enter values up to 7 decimal places for picking the peak.

I would use glucose as an example, which has the formula C6H12O6. What I used is the isotopic mass found on the internet: C12: 12 H: 1.007825 O:15.99491 proton: 1.007276

I ran a negative mode (I believe the most abundance adduct is -H), I calculated the adduct should be 179.0561121, but the reference list supplied by my collaborator is 179.05603.

It would be nice if you have any idea of what mass can I use in order to get the same calculation. I have tried to search online for are there is any mass list that should be used for mass spec, but seems does not help (as I think the mass I use can calculate the mass before ionization, which should be accurate and correct). Thus, I would like to ask for your opinion here before challenging the collaborator.


below are an additional example (I am indeed doing an isotopic tracing experiment): here is a pyruvate (C3H4O3) with 2 carbon labeled with 13C. My calculation is: 12 * 1 + 2 * 13.00335 + 1.007825 * 4 + 3 * 15.99491 - 1.007276 = 89.015478

However, the reference list supplied by my collaborator said it is 89.015396.

  • $\begingroup$ What type of mass spec is that? Do you have five correct decimal places? $\endgroup$
    – ACR
    Commented Dec 3, 2021 at 1:09
  • $\begingroup$ This must be a million dollar mass spec if it is accurate to five decimal places? $\endgroup$
    – ACR
    Commented Dec 3, 2021 at 1:09
  • 2
    $\begingroup$ Well, a hydrogen is a proton and an electron; a proton is just a proton, so the masses should differ by that of the electon. Using a value of $1.6735575\times10^{-27}\pu{kg}$ for hydrogen and $1.67262192369\times 10^{−27}\pu{kg}$ for proton, when I subtract the two I get a difference of $9.35576\times 10^{-31}\pu{kg}$, which is quite close to the (resting) mass of an electron, which is reported as $9.10938356 × 10^{-31}\pu{kg}$. $\endgroup$ Commented Dec 3, 2021 at 1:42
  • 1
    $\begingroup$ Thanks @M.Farooq. I have tried to add more details, I hope I can get the question reopened soon. In short, we are using Thermo Q Exactive PLUS with a HESI source. I believe the adduct is [M-H]-. I have also deleted the hydrogen vs proton question (which is just a side question, and sorry for my ignorance). Ultimately, I just want to know what is the correct mass to use for calculating mass spec weight (or if there is some online calculator). ( indeed, we performed MS in two independent collaborators, and they seem used the same mass for identifying the molecule) $\endgroup$ Commented Dec 3, 2021 at 2:54
  • 1
    $\begingroup$ For [M-H] in negative ion mode, it is M - 1.007276. For monoisotopic glucose in hypothetical negative ion mode, the neutral isotopic mass is 180.0634, so in negative mode as per the link, 180.0634 - 1.007276 =179.0561(2). It matches very closely with your collaborator's number. $\endgroup$
    – ACR
    Commented Dec 3, 2021 at 3:35


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