Great video thanks Brett! I was stuck with DiaNN for a while and this really helped...can you please do a video on analyzing the data using the DiaNN R package?
Thanks for this! A good starting point for using DIA-NN. A note for Sciex users that you need to add some proteowizard files to the DIA-NN directory to process .wiff files. Also, is that a cushion with your face on the sofa??? lol
Thanks for this! I'm totally new to data and analysis in proteomics and this vedio really helps me a lot! But I found that the number of non-zero values in the quantity columns of the pg.matrix file is different from the number of "unique proteins" given in the report.pdf. Why could this happen? What does "unique protein" means?
Thank you @@UCDavisProteomics but I actually found the problem and it was because the lab PC crashed and stopped the run and came back as if nothing had happened... I ran again and it worked.
Really great video! Just starting with DIA on my TimsTOF! Thanks Brett! Lookinf forward for more
Great video thanks Brett! I was stuck with DiaNN for a while and this really helped...can you please do a video on analyzing the data using the DiaNN R package?
Thanks Brett ❤️ You are the best. Thanks for sharing your knowledge and experience across the world generously 🙏🏼
Thank you very much for the video!!
You are welcome!
Thanks for this! A good starting point for using DIA-NN. A note for Sciex users that you need to add some proteowizard files to the DIA-NN directory to process .wiff files. Also, is that a cushion with your face on the sofa??? lol
thanks for the SCIEX info! No I think that's Jeff Goldblum ;)
@@UCDavisProteomicsI bet he would totally be into mass spec, I could see him discussing ions 😂
Or maybe how much of a misnomer “library-free” is !
Thank you Brett for this tutorial. Could you make a video with a analysis after DIA-NN. I mean PCA plot, Differential analysis etc. Thank u in advance
Thanks for this! I'm totally new to data and analysis in proteomics and this vedio really helps me a lot! But I found that the number of non-zero values in the quantity columns of the pg.matrix file is different from the number of "unique proteins" given in the report.pdf. Why could this happen? What does "unique protein" means?
Why DIA-NN results don't show precursor m/z values in report.tsv? Where can I find it?
Could you please explain the process of searching for information related to post-translational modifications in DIA-NN?
Hey Brett.. so my runs are giving me just files.quant. I'm not getting the reports or the tsv files. Do you know whatcould be happening??
I would check the log file. Usually it will tell you what failed or if the reports are saved somewhere else
feel free to send me the log file if you want , I'll have a look.
Thank you @@UCDavisProteomics but I actually found the problem and it was because the lab PC crashed and stopped the run and came back as if nothing had happened... I ran again and it worked.