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.