MSn Quality Trigger filter - MSn Quality Trigger filter - Orbitrap Tribrid Apex Small Molecule Method Editor Help - Orbitrap Apex Small Molecule MS - Orbitrap Tribrid Apex Small Molecule Method Editor Help - Filter types - MSn Quality Trigger filter - Triggers

The MSn Quality Trigger filter, which triggers the next scan only if the MS detects product ion signals that satisfy the specified quality metric and its corresponding threshold or range. You can restrict the product ion signal by the specified Mass Range Mode in the properties pane. For example, the MS might trigger the next scan only if it does not detect enough product ion signals in the range of the TMT reporter ions (that is, m/z 126–131) with a sufficient signal-to-noise ratio (S/N) (for example, a range of 0–200) to produce reasonable ion statistics.

If the proceeding scan has an MSⁿ level of n + 1, the MS performs the next scan on the top N most abundant ions in the spectrum (not necessarily on the product ions that satisfied the trigger conditions). If the proceeding scan has an MSⁿ level of n, the MS performs the next scan on the same precursor ion, but you can vary the subsequent MSⁿ scan settings. For example, if you did not detect enough product signal within a given mass range, you can increase the AGC target and the maximum injection time in the subsequent scan.

The following flowchart shows the MSn Quality Trigger filter.

The following table describes the parameters in the MSn Quality Trigger Properties pane.

Parameter	Description
Quality Metric	The quality metric defines the calculation used for the MSn Quality Trigger. Select one of following quality metric options: Unfragmented Precursor Ion Current Threshold (default) Ion Current Range Signal/Noise Threshold Signal/Noise Range NOTE: To use the "Signal/Noise Threshold" or "Signal/Noise Range" options, select the Orbitrap detector type for the master scan.
Threshold	(Available when the "Ion Current Threshold" or "Signal/Noise Threshold" option is selected.) Specify a threshold value. Range: 0–1 × 10²⁰
Minimum	(Available when the "Ion Current Range" or "Signal/Noise Range" option is selected.) Specify a minimum range value. Range: 0–1 × 10²⁰
Maximum	(Available when the "Ion Current Range" or "Signal/Noise Range" option is selected.) Specify a maximum range value. Range: 0–1 × 10²⁰
Mass Range Mode	(Unavailable when the Unfragmented Precursor option is selected.) Select one of the following mass range mode options: Full Spectrum: Default Mass Range: Specify the m/z range to select the product spectrum. Range: 50–4,000 Range Relative to Parent: The first (start) mass and last (end) mass of a mass range that is positioned relative to the precursor m/z. This value can be located below (-) or above (+) the precursor. Range: –1,000 to 1,000
Mass Range	(Available when Mass Range Mode is set to Mass Range.) Specify the m/z range to select the product spectrum. Range: 50–4,000; default: 350–2,000
Start (m/z)	The first mass of a mass range that is positioned relative to the precursor m/z. This value can be located below (-) or above (+) the precursor. Range: -1,000 to 1,000; default: -5
End (m/z)	The last mass of a mass range that is positioned relative to the precursor m/z. This value can be located below (-) or above (+) the precursor. Range: -1,000 to 1,000; default: -5
Exclude Parent Ion	This will exclude the parent ion from the specified mass range. Default: Deselected
Relative Intensity Threshold (%)	(Available when the Unfragmented Precursor option is selected.) The minimum relative signal intensity required to trigger a data dependent scan. Range: 0–100; default: 20
Mass Tolerance	(Available when the Unfragmented Precursor option is selected.) Defines how close a measured mass must be to the mass in the mass list to be considered the same mass. ppm (default): The low and high values of the mass tolerance width in parts per million (ppm) of the reference mass. This option is appropriate for the Orbitrap mass analyzer because the peak width is proportional to the m/z. You can specify the mass tolerance width as a percent value of the reference mass: First select the ppm option, and then type the desired values in the Low box and High box. The mass tolerance is expressed in parts per million (ppm). When you select ppm, the size of the window around the reference mass is proportional to the m/z of the reference mass. m/z: The low and high values of the mass tolerance width in m/z. This option is appropriate for the Ion Trap mass analyzer because the peak width is constant. You can specify the mass tolerance width in m/z: First select the m/z option, and then type the desired values in the Low box and High box. When you select m/z, the size of the window around the reference mass remains the same regardless of the m/z of the reference mass.
Low	(Available when the Unfragmented Precursor option is selected.) The low side of the mass tolerance width window. The low value defines how far below the reference mass the window starts on the low-mass side of the reference peak. Range (ppm): 0.01–1,000,000; default: 25 Range (m/z): 0.01–100; default: 0.5
High	(Available when the Unfragmented Precursor option is selected.) The high side of the mass tolerance width window. The high value defines how far above the reference mass the mass tolerance window extends on the high-mass side of the reference peak. Range (ppm): 0.01–1,000,000; default: 25 Range (m/z): 0.01–100; default: 0.5
Trigger Type	When 'Continue Trigger' is set and the conditions of the trigger are met, the execution of this branch will continue. If the conditions are not met, the execution of this branch is terminated. Alternatively, when 'Block Trigger' is set and the conditions of this trigger met, the execution of the branch is terminated. If the conditions are not met, the execution of this branch is continued.