msstatsTMT

[KlemensFroehlich]

• Describe the issue or question:

Question: For label-free data, fragpipe offers to export MSSTATS compatible output ( which is really awesome ). Do you think you could also support this for MSstatsTMT ? The input file format is different and requires a lot more info than currently can be specified in fragpipe. So while you can currently set VALIDATION -> GENERATE MSSTATS FILES to TRUE while doing a TMT analysis, it does not generate an msstats output that is compatible with msstats(TMT). Alternatively it would be nice to see in fragpipe that the msstats output can only be generated for non-TMT data.

and off topic: TMT18 plex support would be awesome!

Best Klemens

[fcyu]

We will support MSstatsTMT in the future. Stay tuned!

BTW, for the LFQ data, we recommend using IonQuant in the MS1 Quant tab and not enabling generate msstats files in the validation tab. IonQuant will always generate a MSstats.tsv with LFQ intensities from all experiments.

Best,

Fengchao

[KlemensFroehlich]

Thanks Fengchao for the answer. Looking forward to using fragpipe for everything, including TMT in the future :)

Best, Klemens