MSStats with DIA-NN 2.6 output

[ecirri]

Dear Vadim,

I would like to run DIANNtoMSstatsFormat() with the newest output from DIA-NN 2.6 but I am struggling to find which one to use.
Could you maybe help?

Best regards,

Emilio Cirri

FLI Jena

[vdemichev]

Hi Emilio,

Great to hear from you!

I have never worked with MSStats, I assume it's the main .parquet report, the one you specify in the 'Main output' text field in Output panel. I guess you also need to run DIA-NN with --export-quant supplied in Additional options for MSStats: this provides MSStats with fragment quantities it wants.

Best,
Vadim

[ecirri]

Hi Vadim,

Thanks for following up on this.
I am having a look to a report from DIA-NN 1.8, which was the version I worked more on.
Back then we had the following header:

File.Name | Run | Protein.Group | Protein.Ids | Protein.Names | Genes | PG.Quantity | PG.Normalised | PG.MaxLFQ | Genes.Quantity | Genes.Normalised | Genes.MaxLFQ | Genes.MaxLFQ.Unique | Modified.Sequence | Stripped.Sequence | Precursor.Id | Precursor.Charge | Q.Value | PEP | Global.Q.Value | Protein.Q.Value | PG.Q.Value | Global.PG.Q.Value | GG.Q.Value | Translated.Q.Value | Proteotypic | Precursor.Quantity | Precursor.Normalised | Precursor.Translated | Ms1.Translated | Quantity.Quality | RT | RT.Start | RT.Stop | iRT | Predicted.RT | Predicted.iRT | First.Protein.Description | Lib.Q.Value | Lib.PG.Q.Value | Ms1.Profile.Corr | Ms1.Area | Evidence | Spectrum.Similarity | Mass.Evidence | CScore | Decoy.Evidence | Decoy.CScore | Fragment.Quant.Raw | Fragment.Quant.Corrected | Fragment.Correlations | MS2.Scan | PTM.Informative | PTM.Specific | PTM.Localising | PTM.Q.Value | PTM.Site.Confidence | Lib.PTM.Site.Confidence | IM | iIM | Predicted.IM | Predicted.iIM

I can see now that the report has quite changed (also PG.Quantity is not present, which I was using for Limma in R).
I was wondering if there is a way to somehow reproduce old version of the report with the newest version.

Best,

Emilio

[vdemichev]

Hi Emilio,

The easiest would be to assign columns to fit your scripts, e.g.
df$PG.Quantity = df$PG.MaxLFQ

Best,
Vadim