How to display an MRM or SIR trace in MassLynx and integrate the peaks - WKB125716

OBJECTIVE or GOAL

Display an MRM or SIR trace in MassLynx and integrate the peaks.

ENVIRONMENT

• MasslLynx 3.x
• MassLynx 4.x

PROCEDURE

1. Highlight the sample of interest on the MassLynx sample list (see Figure 1).
2. Click on Chromatogram at the top of the sample list to open the raw data file (see Figure 2).
   • Note: The data initially shows the Total Ion Chromatogram for the first function in the raw data file.
   • If the time range in the x axis is incorrect or "zoomed" in, click on the crossed arrows button on the tool bar.
3. To display the MRM channel of interest, go to Display > Mass from the menu (See Figures 3 and 4).
   • If there are multiple functions in the data file, select the appropriate function from the Functions pull-down menu.
   • Double-click the specific MRM (or SIR) trace or traces to be displayed in the Channels field.
   • The channels to be displayed appear in the Description (chan) field.
   • Click OK.
4. If multiple traces were opened, select the trace of interest by clicking on that Chromatogram (see Figure 5).
   • Note: The selected chromatogram is indicated by a colored square matching the color of the trace to the left of the chromatograms.
5. To integrate the trace, go to Process > Integrate from the menu (see Figures 6).
   • Select the method of integration: ApexTrack Peak Integration (checked) (see Figure 7) or Standard Integration. (ApexTrack unchecked) (see Figure 8).
   • Enter or select the appropriate parameters for Noise/Peak width, Smoothing, Integration (Peak Detect), and Threshold.
   • Click Integrate to process the selected chromatogram.
   • Click Quit to close the Integrate Chromatogram dialog.

ADDITIONAL INFORMATION

Figure 1: MassLynx sample list

Figure 2: Open Chromatogram

Figure 3: Display > Mass

Figure 4: Mass Chromatogram

Figure 5: Multiple Chromatographic traces

Figure 6: Process > Integrate

Figure 7: Integrate Chromatogram (ApexTrack enabled)

Figure 8: Integrate Chromatogram (Standard Integration, ApexTrack disabled)