The Detection Flags and Primary Flags Fields in QuanLynx and TargetLynx Version 4.1

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Randolf Blankenship
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1 TECN New Doc. No. Rev. 01 Page 1 of 5 The Detection Flags and Primary Flags Fields in QuanLynx and TargetLynx Version 4.1 The Detection Flags field in QuanLynx and the Primary Flags field in TargetLynx are optional fields in the browser s Summary Table. Waters recommends that you enable these fields, as they display the status of the quantification, and record any manual changes that you make to the integration and calibration. The following flags may be displayed in the Detection Flags or Primary Detection Flags field: b d s t Peak starts or ends on the baseline Peak starts or ends on a drop line Peak is a shoulder on another peak Peak starts or ends at the start or end of the trace! Manual peak flag m Peak start or end point has been manually altered - Peak has been manually deleted X I Standard has been excluded from the calibration Response is above or below calibration curve (Indeterminate flag) The Indeterminate Flag (I) The I flag indicates that the response falls above or below the calibration curve, and therefore a valid concentration cannot be calculated, as shown in Figure 1. Figure 1 Indeterminate Flag Limits

2 TECN New Doc. No. Rev. 01 Page 2 of 5 Keep in mind that: Responses occasionally fall above the curve when the calibration style is quadratic and the calibration curve is non-linear. Responses occasionally fall below the curve when the calibration style is linear and the curve is not forced through the origin. The calibration curve intersects the Y-axis above the origin. The response is typically close to the detection limits. If there is no calibration solution to the response, and you are using the default browser format, the following fields in the Summary Table will be blank: Conc (calculated concentration) % Deviation (concentration deviation) % Recovery LOD LOQ In the example shown in Figure 2, several responses cannot be quantified, and the Conc field is blank for these samples. Note that all of these rows also display the I flag in the Primary Flags column. Figure 2 Example TargetLynx Summary Table NOTE: In MassLynx Version 4.0, the Conc field displays by default if the response cannot be quantified.

TECN1851799 New Doc. No. Rev. 01 Page 3 of 5 You can choose to display custom text instead of a blank in these fields.

3 TECN New Doc. No. Rev. 01 Page 3 of 5 You can choose to display custom text instead of a blank in these fields. For example, to display ND, right-click on the relevant column and select Edit Column Properties. Enter the custom text in the Default Value field of the Column Properties dialog box (Figure 3). Figure 3 Column Properties Dialog Box Exporting the Concentration When a sample response cannot be quantified and you export the results to XML or to an LIMS txt file, the Conc field is exported as The contents of the Primary Flags or Detection Flags field are also displayed in the pkflags parameter in the exported data, as shown in Figure 4: Figure 4 Example Exported Results You should evaluate any of these flags before accepting the dataset, as there are two known issues that relate to the export of unquantifiable responses: If the response lies above the calibration curve, the zero value that is exported is a false negative. If the response lies below the calibration curve, random concentrations may occasionally be exported as false positives, as described in Technical Note TN The software incorrectly attempts to report a value for the concentration when there is no value in the dataset. These issues will be addressed in the next release of MassLynx for Q-Tof instruments (SCN #639) and Quadrupole instruments (SCN #627).

TECN1851799 New Doc. No. Rev. 01 Page 4 of 5 Additional Features in TargetLynx In MassLynx Version 4.1, TargetLynx includes an additional field that flags samples that cannot be quantified.

4 TECN New Doc. No. Rev. 01 Page 4 of 5 Additional Features in TargetLynx In MassLynx Version 4.1, TargetLynx includes an additional field that flags samples that cannot be quantified. This is the No Solution Flag field, which is also shown in the example TargetLynx Summary Table in Figure 2. This field displays YES if there is no calibration equation solution for the peak (whenever the I flag is displayed). In TargetLynx, the tool tip in the Overview Table also indicates when no concentration has been calculated (see Figure 5). Figure 5 Overview Table Tool Tip Quantifying Samples that Initially Display an I-Flag Modifying the method usually allows unquantifiable samples to be quantified during reprocessing, as follows: If the samples have responses that plot above the calibration curve, you can quantify them by changing the calibration style (for example, from quadratic to linear). If the samples have responses that plot below the calibration curve, you can either quantify them by forcing the curve through zero, or by using an RF calibration. Other Detection Flags that Affect the Calculated Concentration The following flags also affect the contents of the Calc field: The Deleted Peak Flag (-) indicates that the peak has been manually deleted from the chromatogram. If you are using the default browser format, the Summary Table Conc field is blank. The Conc field is exported to XML or an LIMS.txt file as The Excluded Sample Flag (X) indicates that the standard has been manually excluded from the calibration curve. The calculated concentration of all sample types is affected, since the calibration curve changes. The modified concentration is correctly displayed in the Summary Table and exported to XML or LIMS. Conclusion Remember to take the information displayed in the Detection Flags or Primary Flags field into consideration, and always disregard sample responses that are flagged as unquantifiable. This is particularly important when you routinely export results to XML or LIMS files.

5 TECN New Doc. No. Rev. 01 Page 5 of 5

MassLynx 4.2 SCN 989 Release Notes

MassLynx 4.2 SCN 989 Release Notes Page 1 of 20 Waters, THE SCIENCE OF WHAT S POSSIBLE., ACQUITY, Alliance, MassLynx, nanoacquity, and Xevo are registered trademarks and OpenLynx, Quanpedia, and TargetLynx