Non-nested design involves measurements taken from different biological sources or taken at different times—for example, comparing healthy patients to diseased patients. They are not taken from the same sample or samples repeatedly over a course of time.

Procedure

  1. On the Study Definition page, create the study factors to assign to the quantification channels.
  2. For reporter ion quantification and precursor ion quantification, see Add the study factors to the study.
  3. For label-free quantification, see Setting factor values for the samples.
  4. The following example assigns study factors 1 through 30 to the quantification channels.
  5. Study factors assigned to the quantification channels
    Study factors assigned to the quantification channels
  6. On the Input Files page, assign the study factors to the quantification channels.
  7. Select the gray arrow to the left of the first replicate row.
  8. For each quantification channel, select a unique replicate number in the Replicate column.
  9. The following example assigns replicate factor 10 to quantification channel 131.
  10. Assignment of study factors to quantification channels in non-nested design
    Assignment of study factors to quantification channels in non-nested design
  11. Select the Grouping & Quantification tab.
  12. The Generated Sample Groups pane channels (that are grouped by one or more selected study factors) and the Generated Ratios pane of the Grouping & Quantification page confirm that the design is non-nested.
  13. Generated Sample Groups pane showing replicates in a non-nested design
    Generated Sample Groups pane showing replicates in a non-nested design