Separate Library generation vs all in one.

[jsnedeco]

Hello! I am running DiaNN 1.8 on Windows and I noticed something odd, and I was wondering if there was an explanation for it. I basically have two runs.

All in One: Running all the samples at once and using --reanalyze. Separate Speclib: I generate all the quant files separately in parallel on separate machines. Afterwards, using the --temp flag I take all the samples together with their quant files and use the --reanalyze flag.

The results definitely don't come out the same and I also noticed something very strange in the logs when I went to the spectral library generation step. When I generate the quant files separately, I always get 873 spectra added to the library per run. When I generate the spectral library immediately following quant generation I get different numbers of spectra for each sample. I'm definitely getting some noticeable differences between each method, so I'm trying to tease out why they are behaving differently.

separate_speclib.log all_in_one.log

[vdemichev]

Hi,

seaprate_speclib is definitely not normal, some mistake in the configuration. I can take a look if you share the full log?

Please note that 1.9 has a number of integrity checks on quant files that are absent in 1.8, i.e. 1.8 can and will produce nonsense output if the configuration is incorrect (e.g. something change in the settings in comparison to .quant file generation).

Best, Vadim

[jsnedeco]

Here's the separate_speclib.log after the quant files are generated:

separate_speclib_full.log

Here is are logs for two individual quants:

separate_speclib_full_quant1.log separate_speclib_full_quant2.log

Also just to note: this is consistent behavior for different analyses as long as I run this way, in another case, I ended up with 1212 being added per run.

[vdemichev]

This is strange, I cannot pinpoint why this might be happening. I can only suggest for now to switch to 1.9.1, the version 1.8 is a different code base, i.e. cannot debug it now.