The Direct Infusion algorithm is a spectral tree construction utility rather than a component detection method. It allows the creation of one or more spectral trees from a single raw file by the reading of various MSn scans acquired in one run and constructing a tree according to their MS stage and precursor ion m/z values.

To start the spectral tree construction utility using Direct Infusion algorithm:

1. Click on the Components Detection and Spectra Deconvolution button and choose the Direct Infusion pop-up menu item

2. When the parameters setup dialog window appears, change the settings if required, and then click the Calculate button

The Direct Infusion algorithm dialog window contains various parameters that can be optimized for specific types of analysis. Please note that these parameters are interdependent, so a change of one parameter can also affect algorithms linked with other parameters.

Minimal Tree Depth: Specifies the MS stage that should only have a single precursor . The value determines the MS stage where a tree branch division will take place. If the default value 1 is used, the algorithm creates a single tree from all the scans in a run (file). If the value 2 is used and the analyzed run contains MS2 spectra with different precursor m/z values, the algorithm will create separate trees for each MS2 scan with a unique precursor ion m/z value.

Include Upper Spectra: If checked, the resulting spectral trees contain actual scans in the stage above the level set in Minimal Tree Depth. If unchecked, the spectra above the stage set in Minimal Tree Depth. contain spectra with a single peak equal to the precursor ion of the product spectra.

Average Scan: If checked, every tree node will only contain average spectra.

Calculate Envelope: If checked, the ion profile (envelope) for each tree will be calculated. This allows you to preview scans that belongs to particular tree.