This is really a question for Thermo, since they provide the sequest.exe in their Proteome Discoverer. Looking at their Sequest search wizard, they make room for 6 variable mods in their UI, so I wouldn't count on the command-line invocation using sequest.params (what LabKey 11.1 uses) to support any more than 6.

Another approach is to search the same file multiple times with a set of protocols that differ only in their variable modifications. You could use compare peptides to look at the combined results; however they would not be able to be seen in one coverage map.

Peter

I realized I forgot to answer your question on how to specify the variable mods. You can to this most easily through the residue modification section of the Search MS2 data screen. Click on the variable tab and either Add pre-defined modifications or define one not on the list with the New button. This gets written to the tandeml.xml and then gets translated to the right sequest.param values