Improved performance of multiplexed targeted tandem mass spectrometry scans using customized Q Orbitrap data acquisition.

RATIONALE: The Q Orbitrap permits multiplexed targeted selected ion monitoring (SIM) or tandem mass spectrometry (MS/MS) scans. Such scans provide a significantly higher sensitivity than conventional full scan acquisition. However, due to the multiplexing, a monitored product ion extracted from a MS/MS scan can no longer be linked to the precursor ion from which it was derived. Furthermore, due to the automatic gain control, quantification based on targeted product ions acquired in the multiplexed MS/MS mode can become questionable.
METHODS: The application programming interface (API) of the Q Exactive has been used to program a multiplexed targeted MS/MS mode that permits the establishment of a link (based on digital coding) between the product ion and the responsible precursor ion. Furthermore, switching off the automatic gain control feature and the definition of appropriate C-trap settings were tested to improve the quantification performance.
RESULTS: The use of dedicated decoding scans permitted the clear assignment of all monitored product ions to the responsible precursor ion. Furthermore, the customized multiplexed targeted scan used for quantification showed good sensitivity and linearity for a maximum number of eight co-eluting analytes.
CONCLUSIONS: Multiplexed targeted MS/MS scans can be optimized to provide better selectivity (correct linking of an observed product ion to the responsible precursor ion) as well as improved quantitative performance (enforcement of an identical ion injection time for all targeted precursor ions). These two improvements are relevant for quantitative residue analysis.