Do you have experience in creating a protein database for a new proteome? We have a project with a collaborator who has some transcriptomic (RNA-seq) information but there is no (or very little) information available at the protein level i.e. there is not a database that can be downloaded from Uniprot.

We are able to generate .raw MS and MS/MS data for a protein lysate of the organism with ease, but then how does one go about identifying the peptides?

Does anyone have knowledge of de novo sequencing for complex proteomics?

Kind regards, Peter.

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