fcyu
commented
4 years ago Thanks for your interest in our tools.
Yes, IonQuant supports labelling quantification. But both light and heavy labels must have non-zero masses, which means that SILAC is not supported. But dimethyl labelling is supported. What you need is putting the light and heavy mass to the Label field, for example 28.031300;34.063117.
Please note that the labelling support is still in its beta version. Feel free to let me know if there is any question.
Best,
Fengchao
algom
Dear IonQuant developers,
From the Readme file and old publications I read that MSFragger is capable of handling labeled samples (Silac, dimethyl) by adding variable modifications to the search parameters. As for IonQuant it reads "It supports match-between-runs (MBR) and light/heavy chemical labeling" and from the parameters help description and on Fragpipe I see the "label" parameter. Is this correct? If so I wonder how can use it? Does it mean to put the mass, for example in Silac, of light Lysine; mass of heavy Lysine? and then separate by a comma for Arginine? or is it a 0;8.01420,0;10.00827? I was able to run a test file without setting up the "label" option and get quantitations using the LFQ, but as far as I see it is summing up all modifications. I can only see the modifications with the intensities separated in the peptides.tsv.
Thanks for the great work.