Hi All,
This is a question regarding calculation of m/z values of fragment ions from peptide/proteins in mass spectrometry analysis:
1. Does anyone have a recommended tool for calculating m/z values of fragment ions from peptides (such as: input=peptide sequence, output= all y and b-ions, with charge states +1 and +2, etc)?
2. I have previously been using the Proteomics Toolkit on the server: https://db.systemsbiology.net/
This tool is now terminated.
Instead, I have now used the MS/MS fragmentation calculator tool on the server https://proteomicsresource.washington.edu/protocols06/.
However, the two tools do not provide the same m/z values for the same peptide!?
Please see the list below for a direct comparison of the values obtained with the two tools:
Example:
When asking for fragmentation of the peptide with sequence:
GYSEKCCLTGCTKEELSIACLPYIDF
, I get the following results:
Tool 1, Proteomics toolkit calculations (ave mass):
Precursor (M): 3115.34528
Precursor (M+H)+: 3116.35256
Precursor (M+2H)2+: 1558.7
Precursor (M+3H)3+: 1039.45573
Precursor (M+4H)4+: 779.84363
Example of a few selected fragment ions:
Y17(+2): 1008.45486
Y16(+2): 979.94412
Y11(+2): 656.32562
Tool 2, MS/MS fragmentation calculator (ave mass):
Precursor (M): 3115.727440
Precursor (M+H)+:3116.734716
Precursor (M+2H)2+:1558.870996
Precursor (M+3H)3+:1039.583090
Precursor (M+4H)4+:779.939136
Example of a few selected fragment ions:
Y17(+2): 1009.203266
Y16(+2): 980.677606
Y11(+2): 656.804096
As you can see, the two tools do not provide the same values? Which tool provides the correct m/z values and what is going on? :-)
Thank you for your help!
Hi,
This is my go-to site for that purpose: https://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msproduct
Why not look at monoisotopic mass?
The difference in masses obtained can be due to the way the elemental masses are set in the algorithm of the calculator: a difference in digits/rounding can result in large differences in peptide masses, let alone that of complete proteins..!
There is no 'correct' answer, I guess, it's more about the accuracy taken into consideration.
Hope this helps.
Hi Eef,
Thank you very much. Prospectot looks like a good site. It will be interesting to see the difference between the three sites!
I usually find that the "average mass" value fits better with our instruments (Triple-Qs - not high resolution) = produce higher signal than the monoisotopic mass.
Also thanks for the explanation. Rounding error sounds likely.
Best regards,
Jakob
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