Different enzyme for the Novor's parameters

[Fábio CS Nogueira]

Dear DeNovoGUI team,

Congrats for the really nice work.

I have a question about the enzyme present in the Novor's parameters. Please see below:

enzyme = Trypsin
fragmentation = HCD
massAnalyzer = FT
fragmentIonErrorTol = 0.5Da
precursorErrorTol = 10.0ppm

How can I change the default enzyme in this file "novor_params.txt"?

Kind Regards,

Fábio

[Harald Barsnes]

Hi Fábio,

I'm afraid that the enzyme setting cannot be changed for any of the de novo algorithms included in DeNovoGUI. Either it is not supported by the algorithm or the algorithm has to be retrained if a different enzyme is to be used. The good news is that the enzyme setting generally does not have much impact when using de novo sequencing (compared to standard sequence database searches). Hence you should still be able to use the de novo algorithms even if using an enzyme other than trypsin to digest your proteins.

Best regards,

Harald

[Fábio CS Nogueira]

Dear Harald,

Thanks for your quick reply. 

Kind Regards,

Fábio

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Fábio C. S. Nogueira

Professor at Federal University of Rio de Janeiro

Laboratory of Protein Chemistry - Proteomic Unit

Department of Biochemistry, Institute of Chemistry, UFRJ

Av. Athos da Silveira Ramos, 149, CT, Bl. A, 543, Cidade Universitária

21941-909, Rio de Janeiro, RJ, Brazil

Ph: 55 21 39388266 / 55 21 39387353

Laboratory of Proteomics (LabProt) - LADETEC, Institute of Chemistry

Av. Horácio Macedo, 1281, Polo de Química, Bl. C, Lab. 324, Cidade Universitária, 

21941-598, Rio de Janeiro, RJ, Brazil

Ph: 55 21 39383732 / 55 21 39383744