This page describes an iTRAQ quantitation and identification workflow.

Assumptions:

You have recorded iTRAQ data in HCD/CID mode on an Orbitrap hybrid instrument.

What it does:

Peptide quantitation using the ITRAQAnalyzer tool and FDR-controlled identification using three different search engines, which HCD and CID spectra searched separately (for better FDR).

How to run it:

  • Install X!Tandem and OMSSA
  • Make sure X!Tandem and OMSSA executables are in your PATH, or point the 4 adapter nodes to the executables
  • Enter input mzML files in Node #1, and a FASTA database name in Node #8. You also need the preprocessed .phr version of the FASTA file in the same directory (see OMSSAAdapter docu).
  • Enter database and server details for both MascotAdapterOnline nodes
  • Check the parameter settings in every node, especially ‘IDMapper’