How can I quantify efficiency of my extraction method in SCIEX OS software?

For research use only. Not for use in diagnostic procedures.

Answer

Extraction efficiency is the percentage of analyte recovered through the extraction process, from the start of extraction to the final step of sample preparation prior to LCMS analysis. This article explains how to quantify the extraction efficiency in SCIEX OS software.

The efficiency of extraction can be quantified by remembering that the overall spike recovery (quality control (QC) recovery) is a combination of extraction recovery and instrumental recovery (due to the matrix effect):

Overall recovery is the calculated concentration divided by the actual concentration, which is calculated within the results table in SCIEX OS software and displayed in the Accuracy column.

For these fundamental calculations, internal standard (IS) must not be used to correct for the losses in analyte recovery, and true recovery should be calculated without IS correction. When an IS is used, SCIEX OS software will calculate the area ratio (analyte area to IS area) and use this in the calibration curve for determining the calculated concentrations; this will correct for losses in peak area due to matrix effect and extraction inefficiency. To remove the IS from results table calculations, a new processing method should be created where the IS is deselected in the Components tab, and the data should be reprocessed.

For example, if the overall QC recovery is 72%, and the matrix effect causes an instrumental recovery of 80%, then the extraction recovery can be calculated using the equation above:
To calculate instrumental recovery (matrix effect) in SCIEX OS software, see: https://sciex.com/support/knowledge-base-articles/what-is-matrix-effect-how-to-quantify-it_en_us

To understand why extracted samples have a lower signal compared to neat standards, read this link: https://sciex.com/support/knowledge-base-articles/why-do-extracted-samples-and-quality-controls-have-lower-signal-compared-to-neat-standards_en_us