Compatibility with DIA-NN?

[Mengbo-Li]

Hi,
Could I ask if there is any guide on using msqrob2 with DIA-NN main reports?
Thanks,
Mengbo

[ococrook]

Hi!

Thanks for the question, we don't have documentation on this yet. If you have a report you could share, we could certaintly write some documentation that would help!

Best wishes,
Olly

[lgatto]

FYI: we will be adding a QFeatures vignette on how to load and process DIA data produced by DIA-NN. From there, you would have the data in the expected form to proceed with a msqrob2 analysis.

[Mengbo-Li]

Hi Olly,

I quite like this dataset here PXD024043, the DIANN1.8_SingleCells_CellCycle.zip contains the DIANN search results with 20210919_DIANN_SingleCellOutput.tsv being the main report.

The paper this data were published with is here.

Thanks heaps,
Mengbo

[Mengbo-Li]

FYI: we will be adding a QFeatures vignette on how to load and process DIA data produced by DIA-NN. From there, you would have the data in the expected form to proceed with a msqrob2 analysis.

That would be very helpful! Looking forward to that!
Cheers,
Mengbo

[lgatto]

That data is available in scpdata:

library(scpdata)
brunner <- brunner2022()

See also this vignette.