recombinant form of a protein

[GG]

Peptigram is easy to use and really useful on a daily basis for our proteomic platform.

But it works from ProViz which is based on Uniprot. However, we sometimes have recombinant forms of proteins.

Thus, I would like to map identified peptides from a recombinant form of a protein which is not in Uniprot : I have the sequence of this recombinant form expressed in a FASTA format.

Do you know how I can proceed to make this mapping ? Do you plan to incorporate such mapping in peptigram ?

Thanks for your reply.

[Jean Manguy]

Unfortunately I don't have real solution for this problem.

You may try to manually edit your input file using other protein IDs but it's far from being an optimal solution.

The upload of custom fasta files for Peptigram (#2) is something we always wanted to add, UniProt as a source of protein sequences is a huge limitations of Peptigram. ProViz supports custom fasta files but the binding between Peptigram and ProViz necessary to supports custom fasta file requires a lot of time.

As I moved on other projects for my PhD I don't have time, for now, to add features to Peptigram. I want to do it and I will surely do it if I can schedule a full week to work on new features for Peptigram. I cannot give any timeline at the moment.

[GG]

Thanks for your quick answer. Good luck for your PhD.

Do you know any software which can perform such a mapping ? I did not find easy solutions on the internet.

[Jean Manguy]

No, sorry, I'm not aware of alternative that could easily achieve that.