Auto Acquire section (LC/MS)

What do you want to do?

Auto Acquire mode automatically sets optimized instrument parameters and does not require user input. You specify the liquid chromatography method, SIM ions, and/or m/z range for Scan. Source and ion optic parameters are then automatically set. The actual values for the source and ion optics settings in the method are viewed in the method report.

When creating a new Auto Acquire method with an LC configured and saving it (without making any changes to the method), the Audit Trail report shows that the Source parameters changed values. For example, when creating a method, the LC pump default Flow rate is 0.0 ml/min. When the method is saved, the new LC pump flow rate is read and the Source parameters are adjusted. The new Source parameters are then logged in the Audit Trail.

Edit Auto Acquire section (LC/MS)

Edit a method (LC/MS)

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 > MS 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.

Targeted points per second (Hz)

You can enter the desired value for Targeted points per second (Hz). This value along with the Scan mass range and/or SIM masses will be used to acquire data. The Estimated cycle time (ms/cycle) will be updated.

The optimal points across the peak for best peak integration and quantitation is 10 to 15 points across the peak. The Targeted points per second (Hz) should be determined based on the peak width that results from the chromatographic conditions.

Actual 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, or Polarity (if the method is now mixed polarity).

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

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.

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

SIM %

The percentage of each cycle that is used for SIM.

The SIM % value can be any integer equal to or greater than 1 and less than or equal to 100.

If the method does not have any Scan segments, then the SIM % parameter is 100.

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