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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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peptides longer than 30? #409

Open JM-Bader opened 2 years ago

JM-Bader commented 2 years ago

the default peptide length in DIANN is 7-30. image

Clearly, this is an overall suitable range. However, there are often peptides longer than 30. Not that many but due to their length, these are expected to be more likely to be proteotypic and valuable. When creating a DDA-based fraction library with another tool the peptide length range can be longer. In Spectronaut it ranges 7-52 by default. And if I create libraries with Spectronaut or MSFragger (default there is 7-30 as well but of course it can be set to higher values e.g. 7-50) I do get some peptides with longer length.

E.g.: image (MSFragger created)

These tools use the conventional filters and FDR to prevent wrong matches, hence entries in the library, so these longer peptides should also be alright.

Is there any reason not to use these longer peptides in library based searches?

vdemichev commented 2 years ago

This option is adjustable in DIA-NN, can set to any value you like. The primary reason is speed, also I am yet to see a dataset where using longer peptides will be beneficial overall.