Proteome Discoverer output

MonashProteomics / Phospho-Analyst

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Proteome Discoverer output #34

Open mirshahvalady opened 10 months ago

mirshahvalady commented 10 months ago

any thought how we can adopt outputs from PD to be used in this pipeline? the problem with PD output is that the each phospho site location is given within the phosphopeptide and not the protein!

Hailey-Z commented 10 months ago

Hi @mirshahvalady, thanks for your feedback, we have prioritized the compatibility with PD outputs on our list, but it may take some time for the feature to go live.

sooheon commented 2 months ago

Please also consider DIA-NN output, as it has improved phosphopeptide quantification with latest releases.

Hailey-Z commented 2 months ago

Please also consider DIA-NN output, as it has improved phosphopeptide quantification with latest releases.

Hi @sooheon , the compatibility with Spectronaut DIA data is under internal testing and will be updated to the online version soon. Regarding the DIA-NN output, it would be helpful if you have some datasets for testing. My email is: Hailey.Zhang1@monash.edu.

Thank you.