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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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issue with Zeno-SWATH data and protein intensities #840

Open NicoDrou opened 8 months ago

NicoDrou commented 8 months ago

Dear Vadim,

I have some issue to treat data acquired with a Sciex Zeno-SWATH. I did copy all the MS-convert files containing Sciex or core in their name into the DIA-NN folder. I also converted the data into .dia. The search was successful, with all the reports being generated and thousands of proteins detected as expected. However, the protein intensities cannot be correct. Except a few, all intensities are under 1000 and for a dilution series from 1 to 500ng, the detected proteins all have the same intensities, But trust me, the TIC followed the dilution trend :)

Did I forgot to add a command line?

Please find enclose the log file as well as the unique gene report. Zeno-swath.zip

Many thanks in advance for your help

Regards, Nicolas

vdemichev commented 8 months ago

Hi Nicolas,

Intensities are reported in 'arbitrary units' for relative quantification, under 1000 is fine. The protein intensities are reported normalised by default, hence being similar for a dilution series is a good thing :)

Best, Vadim

NicoDrou commented 8 months ago

OMG, indeed, I didn't notice the non-normalized intensities were in accordance with the dilution factor. IS there the same "arbitrary units" effect for other vendors or is it specific to Sciex? I am also using DIA-NN on TIMS-TOF data and i never had this feeling. On the contrary, protein intensities spawn over multiple orders of magnitude.

vdemichev commented 8 months ago

All vendors have different intensity scales.