use peptideshaker for de novo sequencing

[Jing Yuan Shih]

Dear PeptideShaker Team,

I was wondering if it is possible to perform database-free sequencing (de novo sequencing) using PeptideShaker.

If so, can I skip the database input during the input process and still use PeptideShaker to identify peptide sequences from spectra?

I would appreciate any guidance you can provide.

Best regards,
Richard

[Harald Barsnes]

Hi Richard,

PeptideShaker does support the loading of de novo results from Novor and DirecTag, but the results are always mapped to a protein sequence database.

If you just want to look at the de novo result you can however have a look at DeNovoGUI (https://github.com/compomics/denovogui). It is however a bit old and there are probably better tools out there now that do the same thing.

Best regards,

Harald