[Psidev-mod-vocab] Average Molecular Weight of Chemical Modifications in Proteomics Workflows

[Robert W. <rob...@bi...>]

Dear guys,

I am working on protein derivatization chemistry and their subsequent 
LC-MS/MS characterization, and would like to integrate those methods in 
existing proteomics workflows, i.e. PRIDE (Protein MODs) XML, PRIDE 
converter and OMSSA.

Clearly, for the informatics processing we need the molecular weight; 
which is no problem for the mono-isotopic weight, but less trivial for 
the average mass.


These are the values as calculated by the Molecular Weight Calculator:

C14H13N3O2S (Dabsyl Modification)

Monoisotopic: 287.0728438
Average: 287.33804

C22H16N2O7S2 (Uniblue A Modification)

Monoisotopic: 484.0398906
Average: 484.50372

However, different other programs give slightly different results for 
the average mass, e.g. for Uniblue A:

Chemsketch (ACDlabs): av. 484.5016

Online Calculator (Webqc.org): av. 484.5048

1) So, which average weights should we take? For practical applications 
it might not matter, but anyway the information should be consistent.

2) Would it be possible to define the chemical modifications as chemical 
formula, e.g. delta C14H13N3O2S ? So, changed IUPAC values could be 
incorporated easier.

3) Would it be possible for PRIDE to define the chemical modification 
only, and to give the amino acid as an option?

I'm looking forward for your answers and have a nice weekend,

Robert