PeptideShaker Database Requirements (0.22.4 or earlier)

PeptideShaker likes specific format for database if you don’t use searchGUI. They recommend Uniprot database. But occasionally I want to use my own database. There are two specific requirements for correct database in PeptideShaker.

1) It needs decoy sequences.

2)Accession number for decoy sequence has “_REVERSED” tag.

For 1), if you don’t contain decoy sequence, it complains “No Decoys Found”.

decoy-not-found

For 2), if the tag is not correctly added, no unique accession error appears.

Picture1

So the correct fasta format for PeptideShaker is

>IPI000123456.7:protein_description
MEHKEVVLLLLLFLKSGQGEPLDDYVNTQGASLFSVTKKQLGAGSIEECAAKC
EEDEEFTCRAFQYHSKEQQCVIMAENRKSSIII

>IPI000123456.7_REVERSED:protein_description
MEHKEVVLLLLLFLKSGQGEPLDDYVNTQGASLFSVTKKQLGAGSIEECAAKC
EEDEEFTCRAFQYHSKEQQCVIMAENRKSSIII

These requirements are a little bit problematic. I also use IDPicker for MS/MS spectra analysis and it uses decoy tag before the accession number. Well, all I have to do is to create two databases and search with different databases for IDPicker and PeptideShaker.

If you are using searchGUI to search your MS/MS spectrum with OMSSA & X!tandem, you don’t have to worry about these requirements. The software will take care of them.

About bioinfomagician

Bioinformatic Scientist @ UCLA

One response to “PeptideShaker Database Requirements (0.22.4 or earlier)”

  1. Marc says :

    A minor precision:
    By default, PeptideShaker recognizes as decoy all proteins starting or ending with “REVERSED”, “RND” or “SHUFFLED”. In the newest version you can set your own tag 🙂

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