Targeted Loss Trigger filter - Targeted Loss 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 - Triggers - Targeted Loss Trigger filter

The Targeted Loss Trigger filter, which triggers the next scan only if the system detects a targeted loss in the targeted loss list and if all selected conditions are met. If the next scan has an MSⁿ level of n + 1, the next scan is performed on the top N most abundant ions in the spectrum (not necessarily the targeted loss ion). If the next scan has an MSⁿ level of n, the next scan is performed on the same precursor ion, but you usually choose a different fragmentation technique. For example, if you perform a scan with HCD fragmentation and detect a targeted loss that indicates phosphorylation, you can trigger a scan on the same precursor ion but with ETD fragmentation, which provides different product ions. You can also import the settings of the mass list table from (or export them to) a .csv, a .txt, or an .xml file.

The following flowchart shows the Targeted Loss Trigger filter.

The following table describes the parameters in the Targeted Loss Trigger Properties pane.

Parameter	Description
Mass List Type	Select from the following mass list types: m/z M

Mass List Table
Compound	(Optional) Specify the name of the ion.
m/z	(Available when the Mass List Type is set to "m/z".) Specify the m/z of the ion on which the MS performs the scan. When Formula is defined, the m/z is calculated automatically. The accepted m/z range will vary depending on analyzer used (Quadrupole or Ion Trap) and HMRn+ license activation.
Formula	(Available when the Mass List Type is set to "M".) (Optional) Define the compound formula (for example, CH3OH) or peptide sequence (for example, MRFA).
M	(Available when the Mass List Type is set to "M".) The targeted loss mass (in Daltons). Range: 0–100,000; default: 523.2577
z loss	(Available when the Mass List Type is set to "M".) Optional, in some cases. Specify the expected charge state of the precursor ion, which is used to determine collision energy or reaction times (when applicable). When 'Formula' is defined, specify the expected charge state of the precursor ion. This is used to calculate the m/z. Range: 0–24; default: 1

Mass Tolerance	Defines how close a measured mass must be to the mass in the mass list to be considered the same mass. ppm: 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 (default): 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	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	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 Only with Detection of at Least N Ions from the List	Trigger Only with Detection of at Least N Ions from the List. Default: Deselected When selected, the following option becomes available: n: Range: 1–1,000,000; default: 1
Only Ion(s) Within Top N Most Intense	Select to enable only ion(s) within Top N most intense. Default: Deselected When selected, the following option becomes available: n: Range: 1–1,000,000; default: 10
Only Ion(s) Above the Threshold (Relative Intensity, %)	Select to enable only ion(s) above the threshold (Relative Intensity, %). Default: Deselected When selected, the following option becomes available: Range: 1–100; default: 30
Trigger Only with Detection of Correct Charge State of the Product Ion	(Available when the Mass List Type is set to "M".) Performs subsequent scans only if the product ion charge state exactly matches the targeted ion charge state. Default: Selected
Ignore Charge State Requirement for Unassigned Ions	(Available when the Mass List Type is set to "M".) When selected, ions that have an unassigned charge state do not need to meet the charge-state requirement in the table. Default: Selected
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.