Questions for deNovoGUI

[Qin Fu]

Hello,

I'm attempting to sequence a protein that was digested by chymotrypsin. How can I change the settings to avoid the default trypsin?  

Thanks

All the best.

Qin 

[Harald Barsnes]

Hi Qin,

While some of the de novo sequencing algorithms have been trained on tryptic data others do not take this information into account. There is therefore no setting for changing the enzyme used for the digestion as this would generally mean that one would have to retrain the algorithm for this new enzyme. That being said, the de novo sequencing results should not depend too heavily on the enzyme used, especially for algorithms such as DirecTag which only provides sequence tags and not complete peptides.

Best regards,

Harald

[Qin Fu]

Hi Harald,

Thanks for your kind reply. I performed deNovoGUI for chymotrypsin digested .mgf file, seems the results still show the trypsin cutting sites R and K. Do you have any suggestions how to perform deVono of chymotrypsin, GluC et al. digested data? Thanks a gain.

All the best.

Qin

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[Harald Barsnes]

Hi Qin,

> I performed deNovoGUI for chymotrypsin digested .mgf file, seems the results still show the trypsin cutting sites R and K.

Which de novo algorithms are you using? And can you share a screenshot showing where you are seeing the tryptic peptides?

Best regards,

Harald

On Wednesday, February 24, 2021 at 4:18:24 PM UTC+1 fuqin... wrote:

Hi Harald,

Thanks for your kind reply. I performed deNovoGUI for chymotrypsin digested .mgf file, seems the results still show the trypsin cutting sites R and K. Do you have any suggestions how to perform deVono of chymotrypsin, GluC et al. digested data? Thanks a gain.

All the best.

Qin

[Qin Fu]

Hi Harald,

Thanks for your kind reply. I figure out the sequence I want. Thanks again.

All the best.

Qin

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