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

MSⁿ Level (n)

Specify the number of stages of mass analysis.

The options are 2, 3, and n.

Multiplex Ions

(MS² scan type)

Select to perform ion multiplexing. Ion multiplexing performs sequential isolation of multiple ions for simultaneous analysis.

In tMS² multiplexing, the MS uses the quadrupole to sequentially isolate each targeted ion and fragments them as they enter the ion routing multipole (IRM). The MS creates first group of fragment ions in the IRM where they remain as it creates the next group, simultaneously storing them in the IRM. When the IRM contains the fragments from the defined number of multiplexed ions, the MS transports them into the Ion Trap or the Orbitrap for simultaneous mass analysis.

Default: Deselected

NOTE: For tMS², the AGC target value is the total number of ions. Each precursor ion injects for an equal amount of time.

Maximum Number of Multiplexed Ions

(Available when the Multiplex Ions option is selected.)

Specify the maximum number of different ion targets to multiplex for simultaneous mass analysis.

• 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 the target.
• For quadrupole isolation multiplexing in tMS² or for Ion trap isolation multiplexing, each precursor receives the same injection time.

Range: 2–20; default: 2

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.

Define Multiplexing Groups (MSX ID)

(Available when the Multiplex Ions option is selected.)

Select from the following options:

• Off (default): The option is not enabled.
• User-defined: This allows the user to define the grouping for precursor multiplexing in the mass list table. Precursors with the same MSX ID will be multiplexed together. The number of targets in the MSX ID group must be less than or equal to maximum number of multiplexed ions.
• If the user increases the maximum number of multiplexed ions, the MSX ID groups are not regrouped (renumbered) automatically. To automatically regroup the MSX ID, turn the User-define option off and on.
• If the user decreases the maximum number of multiplexed ions, MSX ID groups that are greater than the specified value are flagged in red.

Isolation Mode

Select from the following isolation modes:

• Quadrupole (default): Quadrupole isolation is faster and is done in parallel with analysis, giving the highest instrument duty cycle.
• Ion Trap: Ion trap isolation is fundamental to all MSⁿ analyses (n > 2). Higher-order MSⁿ experiments utilize the ion trap to isolate precursor ions prior to subsequent fragmentation steps.

Select the table icon to add the Isolation Mode to the Mass List Table. When you add the Isolation Mode to the table, the Isolation Window (m/z) parameter will be automatically added. To remove Isolation Window, you must first remove Isolation Mode. Doing so will remove all input data.

NOTE: The Isolation Window can be added to the table independent of the Isolation Mode.

Isolation Window (m/z)

Specify the isolation window for the precursor ions. The allowable isolation window widths differ for ion trap isolation and quadrupole isolation.

• Range: 0.4–5; default: 0.4 (Quadrupole)
• Range: 0.2–5; default: 2 (Ion trap)

The mass range for the peak is centered at the precursor mass and ranges from one-half of the isolation window to either side of the precursor mass.

Narrower windows may result in higher selectivity with fewer interfering ions. Wider windows may result in higher sensitivity as more ions enter the MS per unit time.

NOTE: A value that is too low may result in a loss of sensitivity because not all of the ions in a mass peak or in neighboring isotopic peaks are isolated. A value that is too high may cause interference from neighboring peaks.

Isolation Window (m/z)

Specify the isolation window for the precursor ions. The allowable isolation window widths differ for ion trap isolation and quadrupole isolation.

• Range: 0.4–2,000; default: 0.4 (Quadrupole)
• Range: 0.2–2,000; default: 2 (Ion trap)

The mass range for the peak is centered at the precursor mass and ranges from one-half of the isolation window to either side of the precursor mass.

Narrower windows may result in higher selectivity with fewer interfering ions. Wider windows may result in higher sensitivity as more ions enter the MS per unit time.

NOTE: A value that is too low may result in a loss of sensitivity because not all of the ions in a mass peak or in neighboring isotopic peaks are isolated. A value that is too high may cause interference from neighboring peaks.

Activation Type

Select how the precursor ion is activated for fragmentation.

For more information, see Activation parameters.

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.

Scan Range Mode

(MS² and MSⁿ scan types)

Select the scan range mode to determine the scan range.

• Auto: The last mass is automatically set to the precursor × charge + 10.0. The first mass is set to the lowest value that retains ions at the last mass.
• Define m/z range: Explicitly define the first and last mass.
• Define First Mass: Explicitly define the first mass, and automatically set the last mass to precursor × charge + 10.0.

Scan Range (m/z)

(Available when the Scan Range Mode is set to "Define m/z range".)

Specify the m/z range over which the ion trap or Orbitrap mass analyzer detects ions. Note that the scan range will be automatically added to the table when Detector Type is included due to variations in the analyzer scan ranges. In order to remove Scan Range from the table you must first remove Detector Type.

For CID activation type, the minimum first mass is 145.

Range (Orbitrap and Ion trap): 40–2,000; 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.

First Mass (m/z)

(Available when the Scan Range Mode is set to Define First Mass.)

Specify the first mass (lowest m/z) that will be recorded in the spectra.

Normal Range: 40–2,000; default: 100
High Range: 100–6,000; default: 100

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: 0.001–10,000; default: 1,000

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

Select the mode for the maximum injection time from the following options:

• Auto: When Auto is selected, the system calculates the maximum amount of injection time available to maximize sensitivity while maintaining the maximum scan rate.
• Dynamic: When Dynamic is selected, the system calculates the maximum amount of injection time available to maximize sensitivity while maintaining the desired cycle time.
• Custom: When Custom is selected, the user defines the maximum amount of injection time. This selection enables the Maximum Injection Time (ms) option.

Cycle Time (s)

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

Cycle time is the desired period between acquiring data for each precursor.

Range: 0.6–100,000; default: 3

Desired minimum points across the peak

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

Specify the desired minimum data points required across the LC peak. The system will adjust the injection time to accommodate the desired minimum points across the peak while maximizing injection time.

Use expected "LC Peak Width(s)" divided by "Desired minimum points across the peak" to calculate maximum cycle time.

When Maximum Injection Time Mode is set to Dynamic, the instrument can dynamically increase Time (ms) beyond parallel acquisition when there is time in the cycle remaining.

Range: 1–100: default: 9

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 or Negative option to detect positive or negative ions, respectively, during a scan, but not both simultaneously.

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

Loop Control

Specify the number of scans or the amount of time for each scan cycle (loop) before the MS performs the next experiment, prescan, or both.

This feature is useful for a long mass list. It ensures that the AGC prescans run at regular intervals (once per experiment) for accurate injection times. Each scan cycle consists of one prescan followed by either N targeted scans or as many scans that can run during the specified cycle time. The scan cycle repeats through the mass list from where it last left off. With this feature, you can add another experiment (for example, a full scan) without needing to split up the targeted list.

The options are:

• All (default): Run each cycle on the full list of spectra.
• N: Run each cycle on the next N targeted scans.
• Time: Run each cycle for the specified time.

NOTE: This feature is not available if you add a dependent scan.

N (Number of Spectra)

(Available when the Loop Control is set to the "N" option.)

Specify the number of spectra for each scan loop.

Each scan cycle consists of one prescan followed by either N targeted scans or as many scan that can run during the specified cycle time. The scan cycle repeats through the mass list from where it last left off.

Range: 1–999; default: 20

Time (sec)

(Available when the Loop Control is set to the Time option.)

Specify the cycle time (in seconds) for each scan loop.

Each scan cycle consists of one prescan followed by either N targeted scans or as many scan that can run during the specified cycle time. The scan cycle repeats through the mass list from where it last left off.

Range: 0.2–100,000; default: 3

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.

Time Mode

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

• Unscheduled: An unscheduled targeted scan.
• Start/End Time: A scheduled targeted scan based on the user defined start and end time.
• Retention Time Window: A scheduled targeted scan based on the user defined retention time and window size.