Peptide Length Discrepancy

[Calyx Liu]

Hello!

I was browsing through the documentation, and I noticed that the page for the peptide_length_range param notes the maximum peptide length as 63: Comet parameter: peptide_length_range | Comet MS/MS

However, both the parameter file downloaded from the params page as well as the MAX_PEPTIDE_LEN constant in the code indicate that the maximum length is 51. 

Which number is correct?

Thank you for your time!

Calyx

[Jimmy Eng]

The maximum peptide length was changed to 50 for version 2024.01.0 and newer.  For versions 2023.01.2 and older, the supported maximum peptide length is 63.  The peptide_length_range parameter pages for versions 2024.01.0 and newer have been updated; thanks for reporting this discrepancy.

[Calyx Liu]

Thank you for the clarification Jimmy! Out of curiosity, why was the maximum length decreased? Is there a lot of murkiness for peptides beyond 50 AAs or was it because it is too computationally intense?

[Jimmy Eng]

It was decreased to 50 in order to limit/reduce memory use when the fragment ion indexing support was implemented.