Interpreting peptide sequence output

[KATHERINE MURATORE]

Hello:

I am a new DeNovoGui user. My samples are from an organism without a sequenced genome. I have used the software successfully and obtained a list of spectra and the possible peptides that match to them- but I am looking for a resource to help guide me with what to do next. Specifically, I do not know which peptides are the most likely to belong to my sample. For example, when doing peptide spectral matching data analysis its well documented how to determine what peptides are good hits, etc but I have found relatively little information on how to do something similar with output from Pepnovo+.

If anyone could point me to a tutorial or a paper where this is described, I would really appreciate it!

Thanks

[Thilo Muth]

Dear Katherine,

 

thanks for your interest in using our tool DeNovoGUI. Actually having no information about a reference organism is still a very difficult problem. There are approaches to use de novo sequences by using BLAST or other mapping tools to see whether you can find any (at least far related) organism hits. Besides BLASTing from DeNovoGUI directly, the tool PepExplorer might come handy. It applies pattern recognition approaches when mapping de novo sequencing data against sequences from homologous organisms, see here the paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159663/

 

Here is a more tutorial-like protocol for using the tool:

https://www.ncbi.nlm.nih.gov/pubmed/26334921

 

I never tried it myself... but if you succeed with it, it would be very helpful for us (so you could let us know about it and we can recommend it to more people then...).

 

Good success, best regards,

Thilo Muth