TMT Quantification

[xLinkKnight]

Is it known whether MS Annika can quantify TMT labeled crosslinks? I'm not familiar with the inner workings of PD and what considerations need to go into MS Annika to be TMT quantification capable. Just comparing to XlinkX, I see MS Annika is missing a few nodes in the Consensus workflow. It's a disadvantage of ours to use XlinkX because it's unable to consider more custom Enzyme Cleavage Patterns.

[michabirklbauer]

Unfortunately I have never done TMT crosslink quantification myself and I also don't know anyone who has done that.
But you could try using one of the XlinkX TMT workflows and then just replace the XlinkX nodes with MS Annika. The consensus nodes should all work with MS Annika as well, with the exception of the protein scoring node - which has been bugged since PD 3.1 (see #22).
Sorry to not be able to help more!