Why does MarkerLynx report zero intensity values for some peaks in all injections? - WKB86107

ENVIRONMENT

• MarkerLynx
• MarkerLynx XS

ANSWER

Although it might seem a bit confusing, this is normal MarkerLynx functionality. MarkerLynx uses the Replicate % Minimum setting to exclude peaks that are not reproducibly detected across the full sample set.

From MarkerLynx XS Help files > Creating MarkerLynx XS parameters > Specifying parameters for MarkerLynxXS processing:

"The minimum percentage of samples in a group that a marker must be detected in for that marker's intensity to be used. If the test is not passed , the intensity of the marker is scaled to 0 in every sample in the group. The raw data remain unaffected by the scaling operation.

The number of samples required to satisfy the threshold is rounded up to the nearest integer. For example, if the group contains seven samples and the minimum percentage value is set to 50%, the marker must be detected in a minimum of four of the samples." 

Example

If you set Replicate % Minimum parameter to 0% and process the Mixtures.pro example data positive intensity values for the peak at 3.4453 minutes / 113.9645 m/z are reported in two of the 19 injections (= 10.5% of injections). Now set Replicate % Minimum = 70% and reprocess the data. Because too few samples contain that 3.4453 minutes / 113.9645 m/z peak the detection of that peak is considered irreproducible. It is therefore is reported in the Marker Table of the results and Trend View graph with a value of zero across all injections, including the two injections where the peak does actually occur.

ADDITIONAL INFORMATION

The Replicate % Minimum parameter is missing from the version of MarkerLynxXS bundled with the QTof instrument control versions of MassLynx. This is one of the reasons why QTof users should use only the version of MarkerLynxXS included in desktop processing SCNs for processing their data.

MarkerLynx XS has been discontinued.