Do I need to include all runs in each of my experiment designs?
Progenesis allows you to have multiple experiment designs in each experiment; if after your initial analysis you’ve decided you’d like to compare a subset of the dataset, there’s no need to create a new experiment. Instead, you can just go back to the Experiment Design Setup screen and add a new design. This means you can maximise the statistical analysis you can do on your data without having to run through the entire workflow again.
Other reasons you might not want to include all of your runs in an experiment design are:
- You’ve included additional runs purely for acquisition of ms/ms spectra
- You’ve run pooled samples to aid your alignment
In fact, you don’t even need to include all of your runs in any of your experiment designs; and that includes the first design you make.
Selecting the current experiment design
Where you have multiple experiment designs, you’ll be able to switch between them on various screens (e.g. Review Proteins) using a dropdown list, such as seen here: