How to use the "Find X peaks" feature while avoiding potential integration issues in SCIEX OS.

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

Answer

When you create a reprocessing method in SCIEX OS you can enter a list of targeted compounds by entering different information such as the mass of the precursor and the fragment, the retention time, etc.

When you do not know in advance the retention time of a compound, you can use the "Find X peaks" feature by clicking on the drop-down menu in the Retention time mode column.

In this drop-down menu:

• If we select "RT value", SCIEX OS will use the retention time indicated in the column Retention time (min) to extract peaks. 
• If you select "Find top peak", SCIEX OS will extract the peak with the largest peak area.
• If we select "Find 2 peaks", SCIEX OS will extract the two peaks that have the largest peak area.
• If we select "Find 5 peaks", SCIEX OS will extract the five peaks that have the largest peak area.
• If we select "Find 10 peaks", SCIEX OS will extract the ten peaks that have the largest peak area.
• If you select "Find all peaks", SCIEX OS will extract all peaks.

When using the "Find X peaks" feature, the software may not select the most intense peak. This may be due to a calibration issue with the mass spectrometer as explained in the example below:

In the chromatogram above Sciex OS does not select the most intense peak at 1.75 min which corresponds to morphine. If we manually select the peak which corresponds to morphine, a mass error of 41 ppm is indicated on the precursor (0.012 Da). while the XIC width configured in the Components table for Morphine was 0.02 Da (±0.01 Da).

Due to the elevated mass error, the Morphine XIC fell outside the defined extraction window, resulting in the peak at RT 1.75 min being excluded during the “Find 5 Peaks” algorithm execution.

As an immediate workaround, we recommend increasing the XIC Width setting for Morphine in the processing method’s Components page from 0.02 Da to 0.04 Da. This adjustment restores the expected peak detection behavior, as the observed mass error of 0.012 Da will fall within the expanded window.

For long-term stability and optimal performance, we also recommend performing a full instrument recalibration.