Database Search Exercises > Exercise MSMS2  
 
 

Exercise MSMS2

Topic

Run a target-decoy search to determine false discovery rate

Experimental

Data from a QTof, cysteine residues reduced and alkylated with iodoacetamide (+57). Search Swiss-Prot with precursor and fragment tolerances of 0.3 Da. Loose trypsin with 2 missed cleavages. If using Mascot, check the decoy checkbox on the search form.

Data

Right-click this link: MSMS2.mgf, and choose Save to file

Tips

  • If SwissProt not available, search a mix of mammalian proteins, including human and bovine.
  • Make sure you turn off any second pass search. This would discriminate against the decoy, because decoy peptide matches are scattered randomly across all the database entries

Questions

  1. How many significant peptide matches can you get at ~ 1% false discovery rate?
  2. Change the taxonomy filter or database to green plants. What happens to the FDR? Why do you think this is?

 

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