I looked to excel file results from MaxQuant, and I noticed for example in one protein a list of peptides, when I checked the value of ms m/z it was 840.05 and of ms ms m/z value it was 840.35 why is this difference?I understood that 840 is a precursor ion, and ms ms are fragment ions, In this case, can i say ok this is ms ms spectrum of precursor ion 840.05(see the file, its shown in upper of the spectrum that is ms2 of 840.35 which confused me? I attached part of excel and msms spectrum to help
The MS/MS m/z is the ion that was selected for actual fragmentation while the m/z is the recalibrated precursor mass to charge ratio following the analysis. In essence, the MS/MS m/z (840.38) is straight from the machine so if you were looking for ions at that particular RT you should see that ion. The other value (840.05) has gone through the maxquant m/z correction process and been associated with the peptide its identified as the most likely source of the ionization pattern. ftp://ftp.lrz.de/transfer/proteomics/Phospho_Library/archive/MaxQuant/LibraryResults/HcdNoFilter/combined/txt/tables.pdf
Hi Eric,
which kind of instrument are you using? Might be that MS and MS/MS are detected in different analyzers with different precision?! (such as linear ion trap and Orbitrap)
Best,
Gianluca
Ok, so definitely not... I double checked and basically the delta mass between the two measures that you have for the "same" peptide is 0.33, from your excel sheet it says that the peptide you are interested in a +3 thus, as partially Patrick suggested, it has been selected the second isotope and not the first of the isotopic pattern for the MS/MS fragmentation. [840.38- 840.0478 = 0.33; 0.33 * 3 (charge state) = 1, meaning that the peptide isolated for fragmentation is 1Da heavier]
Hi Eric,
I would expect that the precursor m/z is the peptide's accurate mass, whereas the ms/ms m/z is derived from the isotope that was selected for fragmentation. For larger, multiply-charged peptides, often it's not the lowest isotope that's most abundant - but the most abundant isotope will usually be selected for fragmentation. From the values you've quoted, it could be a triply-charged peptide, and the second isotope peak was chosen for fragmentation.
Let me know if that makes sense or you need a better explanation :)
Malc
Hello,
I also have two different values for MS/MS m/z and m/z. I want to set up a PRM method for my peptides and I was now wondering If I would include MS/MS m/z or the m/z in the inclusion list.
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