And should I tick the "input is from iProphet" if I am using the PTM 
Prophet file generated on the iProphet xml (as input in Protein Prophet)?

On Saturday, August 5, 2023 at 8:32:20 AM UTC+5:30 Debojyoti Pal wrote:

> Hi
>
> I can either input peptide prophet file as input or PTM prophet file as 
> input. What difference will it make?
>
> Regards
> Debojyoti
>

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