Regarding protein prophet input - what difference does it make if I use PTM prophet file or not

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Debojyoti Pal

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Aug 4, 2023, 11:02:20 PM8/4/23
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Hi

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

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Debojyoti

Debojyoti Pal

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Aug 4, 2023, 11:06:10 PM8/4/23
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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)?
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