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Peak Matches are groups of peaks which have been linked (or matched) across your Reference, Control and Target spectra. The matching of peaks can be done either manually or automatically. Peak Matches are the key element of a Screening Dataset.
Open the Hit Analysis module by going to the Screen menu and selecting Hit Analysis or using the shortcut HA. In the DataTable drop-down menu select New Item.... Give your dataset a name and select your Reference, Control and Target (optionally also Displacer) SpectrumGroups. Clicking OK will then add a new DataTable to your sidebar and open a new empty screening dataset in the Hit Analysis module. Alternatively, if you already have an existing Screening Dataset, select that from the DataTable drop-down menu.
You can now start creating Peak Matches which will be added to your screening dataset. This requires the use of the Edit Panel next ot the Peak Binding Scores table. If it isn't already visible, press the Toggle Edit Panel button to make the panel visible. Using one or more SpectrumDisplays, select a set of equivalent peaks in your Reference, Control and Target spectra, click on New/Edit Match in the Hit Analysis module and then OK in the pop-up window. This will add a Peak Match to your dataset which should become visible in your Hit Analysis module tables. You can also select multiple peaks in each spectrum and match them in one go (but make sure you have selected the same number of peaks in each spectrum).
You can automatically create your Peak Matches as part of setting up a screening dataset with the Pipelines module. Open the Pipelines module by going to the Screen menu and selecting Pipelines or using the shortcut PI. Double-click on the Set up Screening dataset pipe in the list of Pipes or drag it into the Drop Pipes area. Give your dataset a Run name and select your Reference, Control and Target (optionally also Displacer) SpectrumGroups. If you are using Reference Singleton spectra rather than Reference Mixtures, leave the Reference SpectrumGroup unspecified and select Use Substance referenceSpectra instead. Now select the Matching Engine of your choice. This is the algorithm used to match the peaks - we usually recommend using the Nearest Match Engine. Finally, select the correct Experiment Type and whether or not to use AutoScale Control-Target Spectra. Run the pipe(line) by pressing the green Play button. Note that this procedure assumes that you have already copied your peaks from your Reference to your Control/Target/Displacer Spectra. For more information about how to do this, see our Hit Analysis Tutorial.
As part of the automatic peak matching, a Peak Matching Score is calculated and provided in the Peak Binding Scores table. These scores represent a quality score for how reliable the matching is. The Peak Matching Scores run from 0-5 with 5 representing a highly reliable match and 0 representing an unreliable match. We recommend that you manually inspect and check matches with a Peak Matching Score of 3 or less. If you find any incorrect matches, you can edit/correct them as explained below.
Each row in the Peak Binding Scores table represents one Peak Match. When you click on a row in the Peak Binding Scores table the linked SpectrumDisplay will automatically navigate to the peaks which make up this Peak Match. If you decide that this is not in fact a good match, you could delete it by pressing the Delete Match button in the Edit Panel of the Hit Analysis module. Then you could create a new (correct) match in its place.
Another way to edit a Peak Match is simply to move the peaks / peak symbols from the incorrect locations to the correct signals (you can do this by right-dragging the peak symbols). You can use Snap to Extremum (SE) or Refit Peak (RP) in the normal way. As soon as any peak locations have changed, the scores and other values in the Hit Analysis module tables need to be updated for that match based on the new peak positions. Either this will happen automatically, or the Update button will turn orange, and you need to press it to update the tables with the new values. Whether the table updates automatically or you need to update it manually can be set with the Auto-Update on peak(s) changed option in the Appearance tab of the Settings.
It is also possible to edit Peak Matches using the New/Edit Match button in the Hit Analysis Edit Panel. If the correct Control peak was matched to your Reference peak, but the wrong Target peak was, you could now select the correct Target peak and then press New/Edit Match. The dialog box will show you the matched peaks on the left and the currently selected peaks on the right. drag the correct Target peak over to the Target peak area on the left and then select Target in the pop-up. Now the incorrect Target peak in the Peak Match has been replaced with the correct one. Again the table will need to update once you have made such an edit to a Peak Match. Whether the table updates automatically or you need to update it manually by pressing the (now orange) Update button depends on whether the Auto-Update on peak(s) changed option in the Appearance tab of the Settings is ticked or not.