LTQ-iQuant

To perform a quantification analysis choose the appropriate option from the File menu.

New Untrained Quantification
This sets up a new quantification from a MzXML file and the corresponding Scaffold report file.
New Trained Quantification
This also sets up a new quantification but additionally requires a training XML file to be specified. Such a file can be created using the 'New Training' option.
New Training
This sets up a new training set for future quantifications from an MzXML file and Scaffold report file with specified expected label proportions.