WARNING: 70655 precursors were wrongly annotated in the library as proteotypic

[Mnago]

Hello, I encountered an issue as described in the title.

Building Spectral Library using DIA-NN v1.9.1

I created a spectral library using DIA-NN 1.9.1 with the following parameters. The output file, report-lib.parquet, serves as the spectral library.

code diann.exe --f "E:\isoform_test\20240205_EV_24minDIA_30F_F1.raw.dia " --f "E:\isoform_test\20240205_EV_24minDIA_30F_F2.raw.dia " --lib "E:\isoform_test\report-lib.predicted.speclib" --threads 44 --verbose 1 --out "E:\isoform_test\report.tsv" --qvalue 0.01 --matrices --out-lib "E:\isoform_test\report-lib.parquet" --gen-spec-lib --prosit --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --use-quant --individual-mass-acc --individual-windows --no-prot-inf --peptidoforms --reanalyse --relaxed-prot-inf --rt-profiling

DIA Analysis using DIA-NN v1.9.1 The corresponding parameters are as follows, and a screenshot of the log file is included below.

code diann.exe --f "E:20240826_LungCa_24minDIA_51.raw

" --lib "D:\human_library_with_isoform\report-lib.parquet" --threads 64 --verbose 1 --out "F:\DIANN191_isoform_libray_based_plasma_serum_report20240828.tsv" --qvalue 0.01 --matrices --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --individual-mass-acc --individual-windows --no-prot-inf --peptidoforms --reanalyse --relaxed-prot-inf --rt-profiling ......

26 files will be processed [0:00] Loading spectral library D:\human_library_with_isoform\report-lib.parquet [0:04] Spectral library loaded: 37043 protein isoforms, 31019 protein groups and 158861 precursors in 142624 elution groups. [0:05] Initialising library [0:05] Saving the library to D:\human_library_with_isoform\report-lib.parquet.skyline.speclib

Why is there an issue with the log file?

Thanks