Quant analysis after de novo

[Nikko]

Hi all,

I'm wondering what are the options for getting quantitative results using peptide sequence from DeNovoGUI.

Specifically, I have some questions:

(1) Is there a tool in DeNovoGUI (or other software) that can convert peptide seqs to protein groups/IDs? I assume a FASTA file is needed for this but what about non-sequenced samples, are there alternative approaches like BLASTing the entire peptide output?

(2) What software is able to give quant data (e.g. MS1 peak area, LFQ) based on DeNovoGUI output sequences?

Thank you all!

-Nikko 

[Harald Barsnes]

Hi Nikko,

In DeNovoGUI you have some options on the Export menu that you can try out for exporting the data and mapping the peptide sequences to proteins. Usually a FASTA file with protein sequences is needed for this to work. However, there is also a BLAST export option that generates a file you can use as input to an external BLAST search. Hopefully one of these options can give you what you want?

When it comes to quantification, there is no direct support for this in DeNovoGUI and I do not have any experience with quantification based on de novo data myself. Perhaps the best option would be to do label free quantification separately and then somehow use the de novo identifications to identify the quantified features? We used to do something similar with Progenisis and identification via SearchGUI/PeptideShaker a long time ago. Not sure whether they still support this kind of workflow though.

Please let us know if you find a quantification pipeline that works for you, as I'm pretty sure others would be interested in this as well.

Best regards,

Harald