Fragpipe about msstatstmt

[devonjkohler]

Thanks Fengchao,

This is an old issue and the converter has been added (and tested with the new Fragpipe output). I am closing this issue for now.

Devon

[tobiasko]

Hi @devonjkohler ,

I am also trying to import msstats.csv written by Philosopher 4.8.1 into MStstatsTMT, see FragPipe issue 510. The FragPipe team told me this currently not possible, but could not really explain why.

Could you maybe comment on why your MSstatsTMT::PhilosophertoMSstatsTMTFormat() function fails to generate complete input data?

Thanks,
Tobi

[fcyu]

Hi Tobi @tobiasko ,

The reasons are simple: there were bugs in the released Philosopher. You can try our pre-released version mentioned in Nesvilab/FragPipe#510

In case you are interested what changes have been made, I did a little search on the https://github.com/Nesvilab/philosopher and found the following commits:

Nesvilab/philosopher@ed401db
Nesvilab/philosopher@95b8e31
Nesvilab/philosopher@f55933e
Nesvilab/philosopher@9b37116

Best,

Fengchao

[tobiasko]

@fcyu THX! Looks like massive code changes and not only restricted to msstats.csv.

[fcyu]

Hi @tobiasko ,

Kind of. As far as I can remember, we 1) fixed bugs in generating msstats.csv (some columns/column names were incorrect); 2) made Philosopher generate a "combined" msstats.csv; 3) made FragPipe generate MSstatsTMT_annotation.csv file (code not included in the Philosopher repository, but in FragPipe repository).

Best,

Fengchao