How do I perform normalisation using an external standard?
If your experiment uses an external standard compound, you can use the external standard concentrations to normalise your samples.
To use external standard normalisation, choose Normalise to external standard in the dropdown on the Review normalisation screen.
You will then be prompted to choose a file containing the external standard concentrations. Progenesis QI supports two file types:
MassLynx .SPL files
The values in the CONC_A field of the sample list will be used as the external standard concentrations.
.CSV files
The CSV file should have two columns:
| Column Name | Description |
|---|---|
| Runs | The name of the run, which must match exactly that in the Normalisation factors table in Progenesis QI (you can right click on this table and choose "Copy table" to copy these values). |
| External standard | The external standard concentration for this run. |
The normalisation factors will then be calculated by:
fi = cr / ci
Where fi is the normalisation factor for run i, cr is the external standard concentration for the normalisation reference determined by Progenesis QI, and ci is the external standard concentration for run i.