terminal modifications in PTMprophet

[MatthiasMuhar]

Dear all,

I am using philosopher to search DDA proteomics data for neo-Ctermini that end on a modification (num_enzyme_termini: 1, variable_mod_05: -0.984016 c^ 1). Search and peptide validation work well, but I would like to estimate the confidence of the called C-terminal modification.

I tried different inputs for the parameter mods ("", " c:-0.984016", " c^:-0.984016", "c:17", "c^:17"), but all gave me errors along these lines:

[ERROR:] Cannot initialize for sequence: LYYIIGDLAGPLLVGRVLLVVLc[17], unknown mods may exist in spectrum 01277_A01_P013129_S00_N01_R1.37332.37332.3
[INFO:] Please specify modification and rerun PTMProphet ...

I therefore wanted to ask: Can PTMprophet be used to validate terminal modifications and if so what would be the correct syntax specifying the modification?

Any help would be highly appreciated. On that note, thanks a lot for the excellent work on the whole "philosopher" platform.

Best,
Matthias

[anesvi]

Sorry, I could not understand why you are trying to localize c-term modification? I suggest you do not use PTMProphet. You do not need it and it may not support c-term modifications Get Outlook for iOS<https://aka.ms/o0ukef>

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________________________________ From: MatthiasMuhar ***@***.***> Sent: Wednesday, February 8, 2023 7:28:39 AM To: Nesvilab/philosopher ***@***.***> Cc: Subscribed ***@***.***> Subject: [Nesvilab/philosopher] terminal modifications in PTMprophet (Discussion #414) External Email - Use Caution Dear all, I am using philosopher to search DDA proteomics data for neo-Ctermini that end on a modification (num_enzyme_termini: 1, variable_mod_05: -0.984016 c^ 1). Search and peptide validation work well, but I would like to estimate the confidence of the called C-terminal modification. I tried different inputs for the parameter mods ("", " c:-0.984016", " c^:-0.984016", "c:17", "c^:17"), but all gave me errors along these lines: [ERROR:] Cannot initialize for sequence: LYYIIGDLAGPLLVGRVLLVVLc[17], unknown mods may exist in spectrum 01277_A01_P013129_S00_N01_R1.37332.37332.3 [INFO:] Please specify modification and rerun PTMProphet ... I therefore wanted to ask: Can PTMprophet be used to validate terminal modifications and if so what would be the correct syntax specifying the modification? Any help would be highly appreciated. On that note, thanks a lot for the excellent work on the whole "philosopher" platform. Best, Matthias — Reply to this email directly, view it on GitHub<#414>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM623VG2DTVDEUSQJPQTWWOGPPANCNFSM6AAAAAAUVGG64M>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[MatthiasMuhar]

Ok. Thanks for the quick response.

For context, I was hoping to get better confidence on that mass-shift originating from the C-terminus itself, as it may arise elsewhere in the peptide (e.g. by D>N or E>Q mutations).

But I see that this is an atypical use of PTMProphet and likely not supported.

Thanks again! Matthias