1 Topic by ggerard

  • ggerard
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Topic: Do fragmentation from a peptide generated in the digestion option

I post here because I ignore if this option is possible, or if it doesn't exist (so this should be moved to the Features forum).

In any case, I think it is only possible to choose between, given a determined sequence, do fragmentation or do digestion.

If I want to do a fragmentation from a sequence generated with a previous digestion, I obviously could manually copy the sequence and perform the fragmentation as if a new sequence it was.

But, I suspect that perhaps this can be done automatically, like clicking twice over the peptide and then, be able to generate the fragmentation, or to import that sequence as a new sequence automatically.

If that's true, how could I do it??

Thanks

PD: If it is a new feature, you could select a number of digested peaks and perform from all of them the fragmentation, then you could do a search within that generated list to match a given list of masses, to be able then to confirm the identification of the digested sequence.

2 Reply by Martin

  • Martin
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Re: Do fragmentation from a peptide generated in the digestion option

Hi,
unfortunately this "workflow" is not implemented for a very simple reason. If you digest a sequence with variable modifications, all the possible variations are generated. Unfortunately, to speed-up digestion and to clean the resulted list of generated peptides, modification positions are not retained. Therefore those peptides cannot be fragmented properly.

I'll look at this soon...

3 Reply by Martin

  • Martin
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Re: Do fragmentation from a peptide generated in the digestion option

In the version 3.9.0, you can copy peptide sequence into a clipboard. Just right-click on a peptide and choose Copy Selected Sequence from pop-up menu.