values in the main output

[hxxhust163]

Hi

Thanks for your work in DIA-NN. I used DIANN-1.8.1 to analyze the DIA files in library-based mode. The library contained 6 fragments for each precursor. Following is the cmd: diann-1.8.1 --dir HYE124 --threads 32 --verbose 4 --out-lib generated-library --gen-spec-lib --out lib-base --lib library.tsv --fasta human_yeast_ecoli_20140403_iRT_reverse.fasta --mass-acc 20 --mass-acc-ms1 10 --smart-profiling --reanalyse --matrices --qvalue 0.01 --reannotate

Then in the main output, I found a strange issue in the 'Fragment.Quant.Raw' column. Some rows of this column contain 12 values, while others contain 6 values. I wonder why this happens as I specify 6 fragments in my library.

Here is a subset of my main result

Thanks very much!

Best wishes xiaoxiang

[hxxhust163]

Here is the first 50 rows of my result. test.csv

[vdemichev]

Hi xiaoxiang,

This looks like some entries in the library have 12 fragments. Can you double check?

Best, Vadim

[hxxhust163]

I checked my library, there are only 6 fragments for each precursor. That is really strange.

Best xiaoxiang

[vdemichev]

Figured out, this occurs as during MBR some library spectra are replaced with spectra extracted from DIA data

[hxxhust163]

ok, thanks very much!