The following example demonstrates how to set up the Study Definition file for a single raw data file with a common channel using TMT 11plex quantification with one study factor for the yeast strain. This example is also described in the Proteome Discoverer Familiarization Guide, Chapter 1 and Chapter 5 (Chapter 5 shows two raw data files).
The file for the single TMT 11plex data resembles the following image.
The study definition file defines a single categorical study factor called Yeast Strain and assigns it to the quan channels.
The File column shows the full path.
NOTE
If the raw data is stored in a different folder, you need to update the path.
The same file is repeated 11 times with the same Quan Method but with different Quan Channels. This is the case for both the reporter ion quantification method and the precursor ion quantification method, where there is more than one quan channel for each file. (For instructions on creating this quantification method, refer to the Proteome Discoverer Familiarization Guide, Chapter 1 and Chapter 5.)