J. Sebastian Paez

I changed the implementation and now it uses a run-length encoded approach to store the precursor information (precursors are stored in order, the number of hits per precursor are stored)....

Made this guy a draft for now! I don't think its worth the current overhead (clear in open search, pretty negligible in closed). Might revisit it later if I see...

As a reference ... https://github.com/lazear/sage/pull/140 this PR added support for dia-pasef direct reading. @jsnedeco (wont discuss diann, since it does a completely different thing) but from what I see in...

All of my samples are 22 min either ddaPASEF/diaPASEF timsrust dda -> discovered 10519 target peptides at 1% FDR timsrust dia -> discovered 3951 target peptides at 1% FDR tdf2mzml...

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 it...

@jsnedeco sorry to hear that. But looking at the glass half full it means it is working! I think we can close this issue and follow up on the progress...

> Just to compare with a direct search of .d folder [using MaxQuant](https://fuzzylife.substack.com/p/proteomics-data-processing-with-maxquant) with https://github.com/user-attachments/files/16439221/fasta.zip, full parameter https://github.com/user-attachments/files/16439180/parameters.txt without LFQ, yield is almost 10 times I am not sure what...

Ohhh I see, thanks a lot for the reply! (It is by no means something critical so dont worry too much about it, just wanted to make sure I was...

Hello there! Since python 2 has reached EOL (as of 2020), do you have any thoughts on the possibility to have the hard-coded path be `/usr/bin/python3` this path seems consistent...

Also ... I f you could point me out to an example of a json-resialized `clusters` and `spectrum_attribute_sets` I would really appreciate it!