Hey everyone. I'm currently trying to replicate what was done in this paper (Article MSFragger: ultrafast and comprehensive peptide identificatio...

) to get a better handle on how to use MSFragger as a tool for analysis in mass-spec. I'm pretty much a newbie when it comes to mass-spec. I am having trouble designing a fasta database for the program to use.

In the methods, it says that " The searched sequence database was created from the human protein sequences of Ensembl version 78 appended with reversed protein sequences as decoys and common contaminants ."

The part that confuses me is the "appended with reversed protein sequences." Should I be taking every single uniprot protein sequence and appending the reverse peptide sequence in this fasta file? I appreciate any help

Cheers,

Yousuf

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