The Targeted Mass Exclusion filter removes the peaks of ions that you list in the mass list. You create a mass list by entering masses and charges in the Mass List table. You can also import the settings from (or export them to) a .cvs, a .txt, or an .xml file.

 

The following table describes the parameters in the Targeted Mass Exclusion Properties pane.

Parameter

Description

Time Mode

Select from the following Time Mode options to enable scheduled or unscheduled targeted scans. For scheduled, the user can define the retention time and window size or the start and end time.

  • Unscheduled
  • Start/End Time
  • Retention Time Window

NOTE: This option is available only if the filter follows an allowable master scan.

Include Intensity Threshold

When enabled, the target m/z intensity must be equal or greater than the specified intensity to exclude.

Default: Deselected

Add Mass List Targets Determined by Xcalibur AcquireX

(Available in Small Molecule application mode when you select "Enable Xcalibur AcquireX method modifications" from the Settings area.)

Enable Xcalibur AcquireX Ab feature for this filter. AcquireX will add targets to the list.

Default: Deselected

Add Mass List Targets Determined by Xcalibur AcquireX Ab

(Available in Peptide application mode when you select "Enable Xcalibur AcquireX Ab method modifications" in the Settings area.)

Enable Xcalibur AcquireX Ab feature for this filter. AcquireX will add targets to the list.

Default: Deselected

 

Parameters in the Mass List Table

Compound

(Optional) Specify the name of the ion.

Adduct

(Available when the Mass list Type is set to "m/z & z".)

(Required when Formula is used) Define the adduct to be used for the defined compound formula or peptide sequence.

m/z

(Available when the Mass List Type is set to "m/z" or "m/z & 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.

z

(Available when the Mass List Type is set to "m/z &z".)

(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

t start (min)

(Available when the Time Mode is set to Start/End Time.)

The time (in minutes) to begin acquiring spectra for the defined target.

t stop (min)

(Available when the Time Mode is set to Start/End Time.)

The time (in minutes) to stop acquiring spectra for the defined target.

RT Time (min)

(Available when the Time Mode is set to Retention Time Window.)

The center of the Retention Time Window (in minutes). For example, when Retention Time is set to 10 and Window is set to 2, acquisition of spectra for the target will only occur between the 9 and 11 minutes.

Window (min)

(Available when the Mass List Type is set to Retention Time Window.)

The window width (in minutes), centered around the defined retention time. For example, when Retention Time is set to 10 and Window is set to 2, acquisition of spectra for the target will only occur between the 9 and 11 minutes.

 

Exclusion mass width

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 exclusion mass 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 exclusion mass 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 exclusion mass 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 exclusion mass width in m/z. This option is appropriate for the ion trap mass analyzer because the peak width is constant.
  • You can specify the exclusion mass 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

Exclude Isotopes

Excludes isotope peaks from consideration for further peak selection.

Default: Selected