ProMass Browser Summary Report

ProMass produces a single top-level summary report (a.k.a., the ProMass Browser Summary), which summarizes the results from an automated processing sequence. The ProMass Browser is linked to each sample and its respective chromatogram summary via hyperlinks. You automatically launch the latest summary report by clicking the ProMass Browser button on the ProMass Home Page. The ProMass Browser summary provides a quick way to navigate the analyses in a particular run sequence. You can even browse the samples by sample plate location with the integrated plate viewer. If you have specified target masses, the status of each of the target masses will be reported in a color-coded format. The status colors are reported based on the logic shown below. Use of the sample plate view is optional and is activated by checking the Show Sample Plate option in the Znova parameter file.

The status colors are reported for each of the target masses specified on the ProMass Browser summary page and on the chromatogram summary page. On the ProMass Browser summary page the best of all status colors will be reported in the result code box. For example, if you specified multiple target masses, one of which was reported as green status, another with red status, and another with orange status, the overall result code for the analysis on the ProMass Browser summary page would be reported as green. Some examples of ProMass Browser and chromatogram summary pages are shown below:

An example ProMass Browser summary page with sample plate view is shown below. Some features are the summary page are:

Clicking on a colored sample well or sample row entry (below the sample plate) will display the detailed ProMass report for the sample.

Clicking on the "ProMass Sample Browser" table heading above the sample plate will toggle the sample plate view.

Clicking on the "Popup View" link at the top left of the sample plate will activate a popup window. Clicking a sample well in the popup window will show the sample report in the main browser window, which allows for rapid screening of the results from a sample plate.

Clicking the table column headings above the sample row entries (e.g., Data File, Sample ID, Sample Comments, Target Masses, etc.) causes sorting of the tables based on the table column heading that was clicked. Clicking a sorted column heading a second time will reverse the sort direction. The default sort of the table is by sample well position.

An example chromatogram summary page with color-coded target mass reporting is shown below. In this example, five different target masses have been specified. The Target Mass Summary table gives information about each target mass including its abundance and location (ret. time) in the chromatogram. Clicking on the hyperlinked entries in the Target Mass or Chromatogram Summary tables will allow you to quickly navigate the report.

Use the ProMass Browser button on the ProMass Home Page to locate the last ProMass Browser summary page processed.

The ProMass Browser summary page is always named index.html and can be found in the promass_results directory of your acquired data directory if you used the default raw Directory Format option. Otherwise, the index.html file can be found in your base Results Directory.

The ProMass Browser summary page is always created for data files processed through the Xcalibur Sequence Setup, but not for individual spectra processed using the manual processing method. A very simple spectrum report is generated for manually processed spectra.

Each data file processed into a particular results directory will be represented by a single row in the top-level summary report. The sample plate view will also be shown if this option is selected in the ProMass parameter file.

If you reprocess data from a sequence row to a particular results directory, any existing summary page will be automatically updated with the new information.

You configure options for the ProMass Browser summary page by editing the options in the Reporting tab in the Build ZNova Params utility. For example, to activate the sample plate view, check the Show Sample Plate option and select the other options for the layout of your sample plate.

Since all ProMass reports are displayed in a web browser, you configure how you want to print ProMass reports directly in your web browser print dialog (File | Print… on the menu). With the default graph size settings (800x600 pixels), ProMass reports are best printed in landscape mode. If you attempt to print in portrait mode using the default settings, the graphics may not fit on the page. If your printer has advanced printing capabilities, you may be able to print several pages on a single sheet. Depending on the printer, these features are usually accessible from the Layout tab in the Print… dialog.

Result Code	Indication
	White. No results available or data not yet processed.
	Green. Target mass found in chromatogram as the most abundant component within user specified mass error tolerance
	Blue. Target mass found as a major component or as a minor component with other target masses, but NOT as most abundant component in chromatogram
	Purple. Target mass found in chromatogram with either or all of the following: (a) other components present in spectrum > user specified % relative abundance (b) low spectral quality ( low intensity and/or score )
	Orange. Target mass found in chromatogram, but NOT as the most abundant in any of the chromatographic peaks
	Red. Target mass NOT found in chromatogram within user specified % mass error tolerance and/or above user specified minimum intensity
	Cyan. No target masses specified