Proteome Discoverer allows users to perform Reporter Ion Quantitation using TMT; the resulting MSF files can then be loaded into Scaffold Q+ for additional analysis. However, PD must be configured properly to maintain functionality. The following notes are taken from the Proteome Discoverer User guide version 2.1 and will ensure data can be successfully loaded into Scaffold (note, the pdStudy or *.param file created by Proteome Discoverer must always be saved in the same directory as the MSF files when running Proteome Discoverer or the Daemon respectively, for version 2.0 and higher).
1. The proper modifications must be selected. When creating a TMT 10-plex experiment the same modifications for a TMT 6-plex experiment are used. All other TMT experiments have there own set of modifications.
2. It is important to note that you cannot have a Reporter Ion Quantifier node (TMT and iTRAQ) and a Precursor Ion Quantifier node (SILAC, dimethyl) selected in the same workflow.
A link to the PD user guide 2.1 can be found here.