Frequently Asked Questions

Analysis


Do I need to create collections to run MaxQuant analysis or can I use single sample inputs?

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.

How can I include custom modifications into MaxQuant in Galaxy?

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.

Which isobaric labeled quantification methods does MaxQuant in Galaxy support?

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.