Proteolabels 1.0 User Guide

Experiment Design

The Experiment Design panel allows you to group replicates together for the purposes of statistical testing. The groupings entered do not affect any other aspects of Proteolabels pair detection or quantification. Proteolabels performs a one-sample t-test over log ratios i.e. testing for deviation from a mean of zero.

Condition The purpose of a condition is to group replicate samples together for the purposes of statistical testing. It is assumed that samples within the same group are biological (or technical) replicates. In designs with multiple conditions, new conditions should be created and Samples moved into Conditions as appropriate.

Sample A sample is assumed to be a biological material that has been labelled and quantified. In a label swap experiment, the same sample might have been labelled with a heavy label in one LC-MS run, and a light label in a different run. The feature Move: "Swap with Sample [X]" should be applied in this case, so that the correct label is associated with the corresponding starting Sample. The effect of this change will be see on the Protein panel, in the calculated t-test p-value and mean across groups (under the Experiment Design drop-down, left panel).

Experiment Settings