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Nonspecific-peptidome #1931

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nishimuy87 opened this issue Dec 11, 2024 · 3 comments
Open

Nonspecific-peptidome #1931

nishimuy87 opened this issue Dec 11, 2024 · 3 comments

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@nishimuy87
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Dear FragPipe team,

Could you please let me know if the nonspecific-peptidome pipeline was designed for tryptic peptides in addition to plasma and CSF samples? I would like to search truncated peptides using FragPipe, but do you know if anyone has tried it already? Any information would be highly appreciated.

Best wishes,
Yusuke
@anesvi
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anesvi commented Dec 11, 2024

Please start with a regular workflow and change to SEMI in the enzyme setting.

@nishimuy87
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Thank you for your response, would you recommend LFQ-MBR with SEMI in the enzyme setting to search truncated peptides?

@anesvi
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anesvi commented Dec 11, 2024

Yes, load LFQ-MBR workflow and change to Semi.

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@anesvi @nishimuy87