For subsequent scans, the Targeted Mass Difference filter selects only ions that have one or two corresponding peaks with mass differences in the target mass list. There are several options that determine which ions to use for subsequent scans.

You create a target mass list by entering mass differences, not the m/z, 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 Difference Properties pane.

Parameter

Description

Number of Precursors in the Targeted Group

Set to define mass difference requirements for precursor sets that contain 2 or 3 targets.

Default: 2

 

Parameters in the Mass List Table

Compound

(Optional) Specify the name of the ion.

Formula

(Optional) Define the compound formula (for example, CH3OH) or peptide sequence (for example, MRFA).

Delta M1

Delta Mass between M1 and M2.

Range: 0–2,000; Default: 8.01

Delta M2

(Available when the "Number of precursors in the targeted group" is set to 3.)

Set to define mass difference requirements for precursor sets that contain 2 or 3 targets.

Range: 0–2,000; Default: 16.02

Partner Intensity Range Relative to the Most Intense Precursor (%)

The intensity ratio (as a percentage) of the partner ion signal intensity to the most intense precursor ion signal intensity that must be exceeded to trigger subsequent analysis.

Range: 0–100; Default:10–100

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

Perform subsequent scan on

For n = 2, the options are:

  • Most intense ion in the pair
  • Lowest m/z ion in the pair
  • Highest m/z Ion in the pair
  • Both ions in the pair

For n = 3, the options:

  • Most intense ion in the triplet
  • Lowest m/z ion in the triplet
  • All ions in the triplet

Charge state requirement

Select from the following options:

  • Ions must be the same charge state: Ions have a mass delta peak or peaks with the same charge state as the target peak.
  • Ions may be a different charge state: No charge state requirement.