jsnedeco

To add to this: I tried out diaPASEF file to just see if I could use something besides DIA-NN for quantification (both for closed source reasons and also because it...

Hi @sander-willems-bruker! I used these parameters: [results_test.json](https://github.com/user-attachments/files/16315185/results_test.json) It looks pretty similar, except your report_psms is a lot higher. I probably can't share the specific .d file I was testing, but...

DIANN was mostly intended as a rough benchmark, not as something to achieve complete parity with :) > PROVIDED THE SAME PARAMETERS FOR SAGE ARE USED, tdf2mzml->sage and timsrust->sage should...

> > Hi @sander-willems-bruker! I used these parameters: [results_test.json](https://github.com/user-attachments/files/16315185/results_test.json) > > It looks pretty similar, except your report_psms is a lot higher. I probably can't share the specific .d file...

> It's also worth mentioning ... Can you share the .tdf without the tdf_bin? It would give information on the instrument, methods and calibration but not the actual scans (technically...

For test 1 it's around 4.1 GB for the .d directory and ~6GB for the mzml. So not a *big* difference, but different.

I got permission to share the raw data for test 1, it is in the same filebin as before labeled test1 https://filebin.net/frqq1bks9pbtzm8s

I can't believe this. I was using the wrong file for the .d input in the first test. I am so mad. Sorry to waste everyone's time, hopefully at least...