Mass Lynks 4.1 Calculation Questions

Hello,I have two questions.1. What settings should I use in my integration method to calculate signal-to-noise? Currently when I incorporated S/N column in my TargetLynx report, I got S/N reported in thousands. Whereas in fact it should be around 20. Also, does it matter for S/N calcualtions if I use smoothing?2. I need to integrate and report peak area% of individual impurities vs. main peak. Data is collected in SIR mode on different channels. I did not find a basic area% integration/reporting option in MassLynx. Should I use "custom formulae" instead, and how?Thank you,Michael


  • Michael,

    1) Take a look at the Signal to Noise calculation method.  RMS (Root Mean Square) will return values much higher than Peak to Peak (generally 3 - 5x greater).  Also, if smoothing is enabled as an integration parameter, S/N will be calculated using the smoothed data.  S/N calculations perofrmed on smoothed data will be much greater than those performed on unsmoothed data.  I generally perform S/N calculations on unsmoothed data but commonly smooth data for integration/quantitation.

    2) A simple Area% report is best handled by OpenLynx.  OpenLynx is a standard feature of MassLynx.

    Good luck,


  • As Rich suggested I would like to share the solution to the area% integration task of individual impurities vs. the main peak in TargetLynx. Here is step-by-step instructions provided by Waters that worked fine for me:

    1. In your method, setup the main compound as you normally would for integration. Then add a compound to the method for each of the impurities. In the Compound Properties, set the Response Type to Internal/Relative. Set the Internal Standard for each impurity as the Main Compound. In the results file, this will put the Area of the Impurity peak and that of the Main Compound on the same line allowing for the use of the Formula fields in the Targetlynx browser.

    2. On the Calibration Properties page for the Impurities, set the Concentration of Standard, Level to Fixed with a concentration of 1.00.

    3. In the Targetlynx Browser Summary Bar, add the column Formula 1.  To do this, right click on the Summary Bar and select Change Column Order from the menu. In the column properties, hit the Formula button. Set the formula to (Peak Area/IS Area)*100. Also in the properties, set the Header to something representative such as % Area or Relative % Area.

    4. Under the file menu from the Browser, go to Save Layout As and give the layout a representative name. The Layout File will save the columns and formula set in the Summary Bar as well as the Report Format for printed reports.

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