use-quant doesn't seem to work

[daichengxin]

Hi @vdemichev. I use the following command to assemble an empirical spectral library from the .quant files. but it doesn't seem to work.

diann --f RD139_Narrow_UPS1_0_1fmol_inj1.mzML --f RD139_Narrow_UPS1_0_1fmol_inj2.mzML --f RD139_Narrow_UPS1_0_25fmol_inj1.mzML --f RD139_Narrow_UPS1_0_25fmol_inj2.mzML --use-quant --temp ./ --smart-profiling --rt-profiling --gen-spec-lib

The .quant files exist in the current directory

[vdemichev]

No spectral library specified => nothing to be done. DIA-NN just exits not doing anything.

[daichengxin]

Hi @vdemichev. I supplemented the library. But a new error appeared. How can I fix this? These libraries are produced by the second step. https://github.com/bigbio/quantms/issues/164

4 files will be processed
WARNING: multiple spectral libraries are specified; this mode is experimental, and DIA-NN does not check if different libraries are in the same format, have consistent modification names or reference RT scales; all libraries must be in .tsv format
[0:00] Loading spectral library RD139_Narrow_UPS1_0_1fmol_inj2_lib.tsv
[0:00] Loading spectral library RD139_Narrow_UPS1_0_25fmol_inj1_lib.tsv
[0:00] Loading spectral library RD139_Narrow_UPS1_0_25fmol_inj2_lib.tsv
[0:00] Loading spectral library RD139_Narrow_UPS1_0_1fmol_inj1_lib.tsv
[0:00] Spectral library loaded: 1551 protein isoforms, 1551 protein groups and 6318 precursors in 5380 elution groups.
[0:00] Encoding peptides for spectra and RTs prediction
[0:00] Predicting spectra and IMs
Predictions generated:
4514
[0:05] Predicting RTs
Predictions generated:
4612
[0:07] Decoding predicted spectra and IMs
[0:07] Decoding RTs
[0:07] Saving the library to empirical_library.predicted.speclib
[0:07] Initialising library

[0:07] Cross-run analysis
[0:07] Reading quantification information: 4 files
E
```RROR: a .quant file was obtained using a different spectral library / different library-free search settings

[vdemichev]

Looks like the initial analysis used to produce the .quant files was performed using a different library.