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tbaccata / amica

amica: an interactive and user-friendly web-based platform for the analysis of proteomics data
GNU General Public License v3.0
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TMT #1

Closed ohovey5 closed 3 years ago

ohovey5 commented 3 years ago

Is this software compatible with Fragpipe TMT experiments?

tbaccata commented 3 years ago

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