Frequently Asked Questions
Collections are not necessary to run MaxQuant but they make the history more clean and easier to navigate. The multiple datasets options allows to select multiple files that are not part of a collection and will give the same result as with a collection as input.
Unfortunately the inclusion of custom modifications is not possible by the user because it requires profound changes in the underlying code. Please let us know the modification you need by creating a new issue: https://github.com/galaxyproteomics/tools-galaxyp/issues entitled MaxQuant new modification request.
The current MaxQuant version supports: iTRAQ 4 and 8 plex; TMT 2,6,8,10,11 plex; iodoTMT6plex. Includion of TMT16 plex is in preparation.