results.mokapot.flashlfq.txt reports Retention time in hours, not minutes

[rodvrees]

As per smith-chem-wisc/FlashLFQ#153 (comment), outputted retention times in the flashlfq input file should be in minutes but for some reason they were written out in hours.

Here's the input file generated by MS2Rescore:

results.ms2rescore.mokapot.flashlfq.txt

[luffy55512]

Hi, I think I’m experiencing the same issue. I also used the flashlfq output file from MS2Rescore as input to FlashLFQ, but all the intensities came out as zero. Could this be caused by the retention times being in hours instead of minutes? May I ask how you resolved it — did you convert the hours to minutes before running FlashLFQ?

Thanks a lot for your help!

[RalfG]

We would have to implement some automatic detection of the RT range based on common lengths, as various PSM file types do not specify the RT units. In the case of very short gradients (e.g., under 2 minutes), this automatic detection would fail. So an override option should be added to the configuration file.

Alternatively, we could verify the RT unit by matching PSM file RTs with the spectrum file RTs.

[RalfG]

I should also note that MS²Rescore does not manipulate the RT values it received from the input PSM file when writing to the FlashLFQ format. So they would only end up in the FlashLFQ file in hours if the original PSM file also used that unit.