Each sample is associated with a quantification channel (shown in the Quan Channel column) and with values for each of the factors that you specified for your study.
NOTE
This only affects reporter ion quantification.
When you acquired the sample, you specified a factor for the acquisition method used and a factor for the tissue that was extracted and labeled. You now set the correct factor values for each of the samples in the Proteome Discoverer application study.
The application supports the following two sample types:
- Sample: A specimen from a larger biological entity. Sample is the default.
- Control: A sample typically used as a reference sample in scaling.
You use the Control type for scaling when the number of samples exceeds the number of quantification channels in the method.
For example, let us say that you used TMT 11plex to acquire 20 samples, and that you created a pooled sample that consisted of all 20 samples for the control. (You performed two runs of 10 samples each plus the pooled sample.) In this case, you would use the Control type to mark the pool as a control channel. The application then rescales the values for the proteins and peptides based on the abundance in the control channel.
An example of this can be found in Proteome Discoverer Familiarization Guide, in exercise 5.