Ion selection optimization for mass spectrometry

The invention discloses a systems and a method for mass spectrometry, and specifically relates to an ion selection optimization for the mass spectrometry. In one embodiment, the method for selecting a target ion and a plurality of qualifier ions for calibration of an analyte in an MS test is presented. For example, the method may include: (a) obtaining a reference spectrum for the analyte; (b) identifying an extraction time window for the reference spectrum; (c) extracting a matrix spectrum over the extraction time window; (d) measuring a noise value in a plurality of matrix ions; (e) calculating a signal-to-noise value for a plurality of analyte ions by dividing the abundance of the analyte ion by the noise value at a corresponding matrix ion; (f) assigning the target ion as the analyte ion having the highest signal-to-noise value; and (g) assigning a qualifier ion as the analyte ion with the next highest signal-to-noise value.