Reporter ion quantification - Proteome Discoverer Software - Reporter ion quantification - Proteome Discoverer Software - Proteome Discoverer Software

The reporter ions quantification workflow contains the Reporter Ions Quantifier node in the processing workflow and the Reporter Ions Quantifier node in the consensus workflow. All of the quantification settings also apply to CSMs and the crosslinks.

Reporter ions quantification is possible with a separate quantification scan, as well as using quan spectra from the MS3 scans. The reporter abundances of a CSM are averaged based on all quantified scans.

For every quantified CSM, the abundances of the single reporter peaks are saved. The aggregation of quan values from CSMs to Crosslinks is done in the same way as quantification values are aggregated from PSMs to Peptide Groups. For Reporter Ion Quantification the following views are available: Quan Spectra View and Quan Channel View.