MS Full Scan - MS Full Scan - Orbitrap Tribrid Apex Small Molecule Method Editor Help - Orbitrap Apex Small Molecule MS - Orbitrap Tribrid Apex Small Molecule Method Editor Help - MS Full Scan - Master scan types - topic

Detector Type

Specify the detector type from the following options:

• Ion Trap: Highest sensitivity
• Orbitrap: Highest resolution and mass accuracy.

Orbitrap Resolution

(Available when the Orbitrap detector type is selected.)

Specify the mass resolution for Orbitrap FTMS analysis. The acquisition time increases with increasing resolution.

The mass resolution of the Orbitrap mass analyzer is proportional to 1/sqrt (m/z).

Mass resolution is defined as the observed m/z value divided by the smallest difference Δ m/z for two ions that can be separated: (m/z) / Δ (m/z).

Spectra acquired at higher Orbitrap resolution allow greater resolution in m/z, however take longer to acquire.

Range: 3,750, 5,625, 7,500, 15,000, 30,000, 50,000, 60,000, 90,000, 120,000, 240,000, and 500,000.

Ion Trap Scan Rate

(Available when the Ion Trap detector type is selected.)

Faster ion trap scan rates have lower resolution. Specify the ion trap scan rate from the following list:

• Turbo: Uses the linear ion trap accelerated scan mode (125,000 Da/sec). When you select turbo scan, the ion trap performs more scans per unit time at lower resolution. This operating mode is useful for increasing the number of scans across a chromatogram peak during a full-scan type, MS scan mode experiment. This increases the total ion count and increases the signal-to-noise ratio for experiments when instrument noise is present.
• Rapid (default): Uses a scan rate (66,666 Da/sec). which is faster than the normal scan. This scan rate is recommended for fast chromatography.
• Normal: Uses the normal scan rate (33,333 Da/sec) and resolution settings.
• Enhanced: Uses the enhanced scan rate (10,000 Da/sec) and resolution settings. This scan rate is an intermediate scan rate between normal and zoom scan. It provides charge state identifications up to charge state 3, which are typically observed with proteomics samples. However, the scan rate is higher than zoom scan, so the scanning throughput is higher than running zoom scan to accomplish this task.
• Zoom: Uses the zoom scan rate (2,222 Da/sec) and resolution settings. Zoom provides information about the charge state of one or more ions of interest. Zoom scans are slower scans with higher resolution than normal scans.

Use Quadrupole Isolation

(MS scan type)

Use quadrupole isolation to have the quadrupole mass filter remove ions before they enter the ion trap or Orbitrap mass analyzer if their m/z values are outside the scan range.

Without quadrupole isolation, ions outside of the scan range may be transferred into the analyzer–using up space charge capacity.

Default: Selected

Scan Range (m/z)

Specify the m/z range over which the Ion trap or Orbitrap mass analyzer detects ions.

Range (Orbitrap and Ion trap): 50–2,000; default: 100–1,000

TIP: As the system optimizes transfer of ions for the defined mass range, it is recommended to restrict the scan range to the region of interest, using a first mass 1 m/z lower than the lightest ion of interest. In addition to the application mode-based defaults, the system templates have recommended application-specific scan ranges.

RF Lens (%)

Specify the value to control the RF amplitude applied to the RF lens.

This value is a scaling factor applied to the nominal mass-to-voltage relationship. Decreasing the RF level decreases the transmission of high m/z ions through the RF lens, increases the transmission of the low m/z ions, and potentially decreases the amount of fragmentation of fragile ions in the RF lens. Increasing the RF level has the opposite effects.

Range: 0–150; default: 60

NOTE: For stable ions, use the default value as a starting point. The different MS models have a different design for the RF lens, resulting in different values for the RF lens parameter. Consider this when you set the RF lens value.

AGC Target

The automatic gain control™ (AGC) target value controls the number of ions that are injected into the Orbitrap or Ion trap mass analyzer for mass analysis.

Select from the following options:

• Standard: When Standard is selected, the system sets the recommended target in an automated fashion per scan type and user-defined settings.
• Custom: When Custom is selected, the user defines the target. This selection enables the Normalized AGC Target (%) option.

Absolute AGC Value

The Absolute AGC Value is a conversion of the AGC percentage target set in the method into absolute values. It is a read-only value and is automatically updated according to the scan type and the target percentage.

Normalized AGC Target (%)

(Available when the AGC Target is set to Custom.)

Specify the automatic gain control (AGC) target. This is a percentage representing the maximum number of charges to accumulate for a given analysis.

Range: 0.001–1,250

The normalized AGC target value is represented as a percentage to aid in calculating the desired AGC target. The base normalized value is different for MSⁿ Level and Detector Type. The values are as follows:

• Scan Type: Full Scan
• Normalized Base (100%), Orbitrap detector = 4e5
• Normalized Base (100%), Ion Trap detector = 3e4
• Scan Type: SIM Scan, MSⁿ Scan
• Normalized Base (100%), Orbitrap detector = 5e4
• Normalized Base (100%), Ion Trap detector = 1e4

The ion routing multipole (IRM) fills ions until it reaches the AGC target or the maximum injection time. The MS then transfers the ions to the Ion Trap or Orbitrap for analysis.

Some scan types allow multiplexing.

• For quadrupole isolation multiplexing in tSIM, the total AGC target is per ion species of a multiplexed group. Each species will inject for different times in order to achieve target.
• For quadrupole isolation multiplexing in tMS² or for ion trap isolation multiplexing, each precursor receives the same injection time.

NOTE: The dynamic range of tMS² multiplexing is more limited than tSIM multiplexing because the injection times of all precursors are equal. Also, Ion Trap isolation multiplexing is in general much less well developed and should be regarded as an experimental feature.

When "Standard" is selected for AGC target, the system will set a recommended value for the scan type. This may deviate significantly from the default 100% Normalized level.

Maximum Injection Time Mode

Specify the maximum injection time mode for AGC from the following options:

• Auto (default): The system calculates the maximum amount of injection time available to maximize sensitivity while maintaining the maximum scan rate.
• Custom: The user defines the maximum amount of injection time. This selection enables the Maximum Injection Time (ms) option.

The ion trap fills with ions until either the AGC target or the maximum ion injection time is reached.

Maximum Injection Time (ms)

(Available when the Maximum Injection Time Mode is set to Custom.)

Specify the maximum injection time (in milliseconds) allowed to reach the AGC target.

Range: 0.001–8,000

The ion routing multipole (IRM) fills ions until it reaches the AGC target or the maximum injection time. The MS then transfers the ions to the Ion Trap or Orbitrap for analysis.

Some scan types allow multiplexing.

• For quadrupole isolation multiplexing in tSIM, the total AGC target is per ion species of a multiplexed group. Each species will inject for different times in order to achieve target.
• For quadrupole isolation multiplexing in tMS² or for ion trap isolation multiplexing, each precursor receives the same injection time.

NOTE: The dynamic range of tMS² multiplexing is more limited than tSIM multiplexing because the injection times of all precursors are equal. Also, Ion Trap isolation multiplexing is in general much less well developed and should be regarded as an experimental feature.

Microscans

Specify the number of microscans per scan.

A microscan is one ion injection followed by ion detection. The MS sums microscans to produce one scan, which improves the signal-to-noise ratio of the mass spectral data.

Range: 1–5,000; default: 1

NOTE: The overall scan time increases linearly with the number of microscans, significantly slowing the rate of spectral acquisition.

Data Type

Specify how to collect data during the currently selected scan event using the following options:

• Profile: The profile data type is represented by a collection of signals over several scans. The advantage of profile data is it is easier to classify a signal as a true peak from noise off the instrument.
• Centroid (default): The centroid data type replaces detected peaks with a single m/z and intensity pair, which results in smaller file sizes.

Polarity

Select the Positive, Negative, or Both option to detect positive ions or negative ions during a scan, or both (in sequential scans), respectively.

NOTE: The polarity mode applies to the entire experiment (workflow). Each experiment can have different polarity settings.

Source Fragmentation

Select to turn on ion source fragmentation.

An offset voltage in the ion source accelerates the ions into the background gas. Collisions with the background gas might aid in the desolvation of the ions and increase sensitivity.

If the source fragmentation is set too high, fragmentation of ions may occur.

Default: Deselected

Energy (V)

(Available when Source Fragmentation is selected.)

Specify the collision energy voltage for ion source fragmentation.

An offset voltage in the ion source accelerates the ions into the background gas. Collisions with the background gas might aid in the desolvation of the ions and might increase sensitivity. If source fragmentation is set too high, fragmentation of ions may occur.

Range: 1–100; default: 35

Scan Description

Type an optional description for the selected scan node. This scan description then appears in the scan header of the spectrum’s raw data file.

You can leave the field blank. However, if used, the scan description must be unique within the method and have a maximum of 16 characters. You can use alphanumeric characters, commas, hyphens, parentheses, periods, plus signs, spaces, and underscores.