The RT range in the spectral library is inconsistent with the actual DIA data.

[atesora]

Hi Vadim, Thanks for this amazing software. I want to analyze DIA data using a DDA library that was constructed from MSFragger. The actual LC gradient is 40 minutes, but after building the library, the RT in it is 120 minutes. When I use this DDA library to analyze DIA data with 40 minutes LC gradient, the results come back empty. I would like to know if DIANN supports matching DIA data with spectral libraries that have different LC gradients.

I am looking forward to your reply. Thank you for your help!

[vdemichev]

Hi,

Can you please share the full log? I can they try to see what's wrong. DIA-NN supports any kind of libraries regardless of the gradient.

Best, Vadim

[atesora]

Hi Vadim, Thank you for your quick response. Here are the logs. report.log.txt Thanks！

[vdemichev]

The main report is not empty here. If pg_matrix is empty, this is because no protein groups are identified confidently enough. Still fine, you can just use whatever DIA-NN outputs in the main report. However, ideally you would want to increase the total number of identifiable peptides. For this, when you are generating the DDA lib, good to make sure that you are also searching at least for common contaminants or whatever else might be detectable in the sample.

Best, Vadim

[atesora]

Thanks Vadim, Yes, results are only found in the report.tsv and report-first-pass.tsv files. The database used for the DDA library construction includes decoys and contaminants. My goal is to count the number of identified modified peptides. Can I analyze the results in the report.tsv or report-first-pass.tsv files for this purpose? Thank you very much!

[vdemichev]

Can I analyze the results in the report.tsv or report-first-pass.tsv files for this purpose?

Yes!

[atesora]

Thanks for your help！

Best， Chenfang