The following table describes the parameters in the Peak Selection area of the Component Detection page.

Peak Selection area parameters



Peak #

The Peak Selection area contains a section (Peak #) for each peak you add to the top down analysis.

Select the appropriate Peak # section before defining its corresponding parameters.

RT Range

Specifies the beginning and end retention times (RT) of the range of the each peak you add to the top down analysis.

You can either type the range values or select the range of each peak from the chromatogram in the Chromatogram pane. For multiple raw data files, select the range for the first file to apply the range to all of the loaded files.

Scan Filters

For an experiment with a single loaded raw data file, this parameter displays the scan filters available for the entered RT Range, Intact Fragmentation (required), and Intact Deconvolution (optional), which the application automatically reads from the file.

For Intact Fragmentation, the filter is applied per peak. Select one filter from the Intact Fragmentation list. The application uses the selected Intact Fragmentation filter and the features of the ProSight Lite application to process MS2 data.

For Intact Deconvolution (optional), the filter is applied per raw data file. To perform deconvolution of the full-scan MS spectrum, select the Intact Deconvolution checkbox and then select one filter from this list. The application uses the selected Intact Deconvolution filter to process the Full MS scans, similar to intact mass Analysis.

For a multiconsensus experiment with multiple loaded raw data files, select the Multiple File Parameters button (...) to open the Multiple File Parameters dialog box. This box displays a table with the data from each loaded raw data file, including the file name, scan filters, and activation types. From the table, select the appropriate scan filters and Activation Type for each file, and then select OK.

In the pop-up box for multiple files, you might not be able to see the entire name of a raw data file if the name is long. In this case, hover your cursor over the file name in the table to view the entire file name.

If no scan is present for the specified RT Range, the Scan Filter list is empty.

Activation Type

Displays the list of available fragmentation methods for your selection.

For a single loaded raw data file, the default fragmentation type appears automatically from the selected Intact Fragmentation scan filter, if available.

For multiple loaded raw data files, the application automatically derives the default fragmentation type.

You can retain the default value or select a different fragmentation type as needed.

Fragmentation types include CID, HCD, SID, ETD, ECD, ETHCD, IRMPD, and UVPD. See Fragmentation methods.

Protein Sequence

Displays the protein sequence(s) selected in the Protein Sequence area of the Top Down Analysis page. From this list, select one sequence for each peak.

The application automatically searches all proteoforms saved with the selected sequences.

If you select a single protein sequence on the Top Down Analysis page to use for the experiment, the application displays this sequence as selected for the current peak by default.

If you selected multiple protein sequences on the Top Down Analysis page and you select an Intact Fragmentation scan filter, you must explicitly select a protein sequence for each peak before processing the experiment.

Fragmentation Mass Tolerance

Specifies the fragmentation tolerance for the MS2 scan (in Da or ppm) within which the masses of the sequence and a component must fall to be considered a match.

For example, if you set your tolerance to 0.005 Da and your theoretical fragment ion is at 1154.1126 Da, the observed fragment ions of 1154.1090Â Da (−0.0034 Da from theoretical) and 1154.1167 (+0.0041Â Da from theoretical) fall within the tolerance, but 1154.2312 (+0.1222 Da from theoretical) does not because the mass difference is greater than your specified tolerance.