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MonashProteomics / FragPipe-Analyst

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Experiment annotation for gas-phase fractionated samples? #73

Closed jossmi closed 1 year ago

jossmi commented 1 year ago

Hi, I have gas-phase fractionated DIA samples and have updated my experiment-annotation.tsv file to have each fraction within a sample assigned to the same replicate (see attached; the "PAA_X" value represents fraction 1, 2, or 3; also, I have saved it as a .csv because GitHub won't let me attach a .tsv, but I have been using the .tsv format when submitting to FragPipe-Analyst). However, it doesn't appear to be working correctly, as the report lists all fractions as individual samples, rather than combining them together within a sample. Accordingly, there is a lot of data listed as missing, since it seems it is treating fractions as individual samples. I thought I saw a way to handle fractions in the tutorial, but I can't find it now. How can I get FragPipe-Analyst to properly pool fractions within samples?

Thanks, Josh

experiment_annotation_example.csv

hsiaoyi0504 commented 1 year ago

@jossmi Sorry, we currently don't support that. We might improve this in our DIA data processing in the future.