TMT

[ohovey5]

Is this software compatible with Fragpipe TMT experiments?

[tbaccata]

Thanks for showing interest in amica!
So far, amica has only been tested with FragPipe's LFQ workflow. By default, amica can parse FragPipe's combined_protein.tsv output. Looking at the TMT example in FragPipe's doc (https://fragpipe.nesvilab.org/docs/tutorial_tmt-2plexes.html#analyze-the-whole-proteome-samples), the TMT workflow also outputs a combined_protein.tsv file. Testing this with the example TMT combined_protein.tsv file, amica is able to read in and analyze this output.

Best,
Sebastian