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The acquisition software allows one to select to automatically have the system go to standby mode, which turns the pump(s) and the ion-source voltage and spray temperature off. Meanwhile, the ion-transfer tube temperature remains on and a low flow of nitrogen blows across its entrance. This minimizes the chances of letting contaminated ambient air enter the mass spectrometer.

The software will show pressure traces to ensure that the pumps are working properly. Reproducible retention times and area counts for each of the internal-standard peaks ensure that the injector, LC column, and mass spectrometer are working properly. Results for each calibrator must pass acceptance criteria and results for each quality control (QC) must be within acceptable limits to report sample results while being within the specified analytical range of the calibrators. The calibrators must also pass acceptance criteria for chromatographic peak integrity (actual vs. expected retention time and ion ratio confirmation) to ensure reliable quantitation.

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