When using a Targeted Loss Inclusion filter, if the system detects a targeted loss ion in the targeted loss mass list, and if all other conditions that are selected are satisfied, the filter triggers an MSn+1 scan on the targeted loss ion. You can also import the settings of the mass list table from (or export them to) a .cvs, a .txt, or an .xml file.

The following figure shows a flowchart of the Targeted Loss Inclusion filter.

 

The following table describes the parameters in the Targeted Loss Inclusion 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 (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

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: 10
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: 10
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