Advanced Acquire > Acquisition section (LC/MS)

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User Interface - MS Global Parameters Pane

Each section in the SQ section of the Method Editor has two panes. The MS Global Parameters pane is the top pane in the Instrument Setup > SQ > Method section. It is visible when any of the Instrument Setup > SQ > Method sections are visible. See Advanced Acquire > Global Parameters Pane (LC/MS).

User Interface

You set the Scan type in each row of the Acquisition Parameters table. Different columns are available for Scan rows and SIM rows.

Acquisition Parameters Table

The following information is available in the Acquisition Parameters table. If you click a column header, the table is sorted by that column. If there is an error caused by the current editing cell, then the current editing cell is shown in pink, and the tooltip shows additional information. If a validation error exists, you cannot save the method.

Time (min) - the time to start acquiring the SIM signal. The Scan signals are collected through the entire run, so this value is not available if the Scan type is Scan.
Scan type - Scan or SIM. The contents of the row change depending on this selection. You can only have four rows which have a Scan type of Scan.
Polarity - either Positive or Negative.
Compound/Segment name
Mass range start (m/z) - See Scan range (LC/MS). This value is only available if the Scan type is Scan.
Mass range end (m/z) - See Scan range (LC/MS). This value is only available if the Scan type is Scan.
Mass (m/z) - the mass to use when the Scan type is SIM. This value is only available if the Scan type is SIM.
Quad res - Unit, Wide, or Widest. You select the option for the quadrupole resolution. This value is only available if the Scan type is SIM.
Scan/Dwell time (ms) - This calculation is based on the Targeted points per second, mass range, and SIM %.
Detector Gain Factor - See Detector Gain Factor (LC/MS). If the converted EMV from user-defined Detector Gain Factor reaches or exceeds the maximum value of EMV (3000 V), the EMV will be set to the maximum.
Fragmentor (V) - See Fragmentor (LC/MS). If this value is Ramp, see Advanced Acquire > Ramp Table (LC/MS).
Fragmentor ramp? - whether or not to use the Fragmentor ramp for this scan. If you select this option, click to see the Advanced Acquire > Ramp Table (LC/MS). This value is only available if the Scan type is Scan.
ISTD? - whether or not this SIM segment is an internal standard. This value is only available if the Scan type is SIM.
Threshold - the threshold to use for the Scan segments. Determines how large a signal must be before it is reported. Typical values are between 0 and 500. This value is only available if the Scan type is Scan and the Data storage is Centroid.
Ion mode - the ion mode if you have a Multimode ion source installed. The MMI source is not supported on the LC/MSD iQ.

Targeted points per second (Hz)

When you check this box, you enter the points per second that you want to achieve in the Targeted points per second (Hz) parameter. If Scan and SIM Scan Types are present, the SIM % is editable. The Scan/Dwell time (ms) is calculated based on the Targeted points per second (Hz), the Scan mass range, and/or the SIM mass, and SIM %. Changing any of these values will result in different Scan/Dwell time (ms).

The optimal points across the peak for best peak integration and quantitation is 10 to 15 points across the peak. You should consider the peak width that results from the chromatographic conditions when setting the Targeted points per second (Hz).

When you clear the Targeted points per second (Hz) check box, you can enter the desired value for Scan/Dwell time (ms) for all Scan types.

Actual targeted points per second (Hz)

You can select one of the predetermined values for targeted points per second (Hz).

One to 15 data points of matching possible points per second are provided for you. The calculations are based on the number of points, mass fields, polarity, and tune file values. You input the points per second in the text box, and the software uses that value to calculate the nearest actual points per second value and populates the Actual points per second (Hz) values. The Actual targeted points per second (Hz) value closest to the Targeted points per second value (Hz) is selected for both. When no value is possible for the actual point per second, the error message is displayed in the SIM % parameter.

The purpose of the actual points per second value is for you to have a choice of points per second close to the targeted points per second you entered that accurately reflect the actual data acquisition rates that the instrument will achieve.

Estimated cycle time (ms/cycle)

The Estimated cycle time and the scan speed are estimates.

Displays the calculated time (in milliseconds) to execute all active signals once. This may also be thought of as the time between chromatographic data points in each of the programmed signals.

The Estimated cycle time (ms/cycle) is automatically updated when you change the Start mass, End mass, Polarity (if the method is mixed polarity), or Scan/Dwell time.

The cycle time is calculated automatically using the number of masses in the table and the dwell time.

Data storage

Centroid or Profile. With Centroid, you are recording the mass to charge and the abundance at the mathematical center of mass of the analog data. A single m/z and abundance data point is recorded. With Profile, all filtered raw data is saved. This uses more disk space than Centroid data (a larger data file is created). You use Profile for multiply charged samples or when spectral averaging is used extensively. With Profile, the Threshold for Scan rows is not used.

If the method does not have any Scan segments, then the Data Storage parameter is not available.

Estimated max scan speed (Da/s)

You cannot set the scan speed directly; it is a calculated based on other parameters such as scan ranges, SIM %, and the actual points per second. It is a calculation of how fast the mass filter is scanning.

If Targeted points per second (Hz) is selected, then the Estimated max scan speed is updated when you change Mass range start, Mass range end, or add a SIM row in the Scan table. It is also affected, by the SIM % value and the Targeted points per second (Hz) value.

If you clear the Targeted points per second (Hz) check box, then this value is also affected by the Scan/Dwell time (ms) in the table.

If the mass range of any of the rows (Mass range end - Mass range start) increases, then Scan speed increases. If you increase the number of scan segments , then the Scan speed increases.

If the method does not have any Scan segments, then the Estimated max scan speed (Da/s) parameter is not available.

SIM %

The percentage of each cycle that is used for SIM. When you select Targeted points per second and both Scan and SIM types are in the table, then you can edit this value. When you edit this value, the Scan/Dwell time (ms) is changed. Also, if you edit the SIM % value, you may also need to edit the Targeted points per second (Hz) value.

If you manually change the SIM % value, this value is remembered if you uncheck and then check the Targeted points per second (Hz) check box.

The SIM % value can be any integer equal to or greater than 1 and less than or equal to 99.

If the method does not have any SIM segments, then the SIM % parameter is not available.

User Interface - Toolbar

This toolbar is available for both Scan and SIM rows in the Acquisition Parameters table.

Toolbar icon	Action
	Add a row to the table
	Insert a row in the table
	Remove the selected row from the table
	Copies the selected cell to all of the other cells in the column
	This feature is not available.
	Copies the selected rows/cell of the table
	Pastes the rows/cell from the Clipboard