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.
Set the Scan type in each row of the Acquisition Parameters table. Different columns are available for Scan rows and SIM rows.
The following information is available in the Acquisition Parameters table. Click a column header to sort the table by the 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. If signals are specified in the Fraction Collection Trigger Signals table, you must enter a value of 0 for all SIM scan segments.
Scan type – Scan or SIM . The contents of the row change depending on this selection. You can only have four rows that have a Scan type of Scan. If signals are specified in the Fraction Collection Trigger Signals table, you can only have two rows that have a Scan type of Scan and only 200 rows with a Scan type of SIM.
Polarity – Either Positive or Negative .
Compound/Segment name
Mass range start (m/z) – See Scan range. This value is only available if the Scan type is Scan. The scan mass range is 2–3000 for Pro iQ and 2–1600 for Pro iQ Plus, with a step size of 0.1.
Mass range end (m/z) – See Scan range. This value is only available if the Scan type is Scan. The scan mass range is 2–3000 for Pro iQ and 2–1600 for Pro iQ Plus, with a step size of 0.1.
Mass ( m/z ) – The mass to use when the Scan type is SIM. This value is only available if the Scan type is SIM. he scan mass range is 2–3000 for Pro iQ and 2–1600 for Pro iQ Plus, with a step size of 0.1.
Quad res – Select the option for the quadrupole resolution to control the mass window and peak width. This value is only available if the Scan type is SIM.
Narrow: 0.4 Da (available only for Pro iQ and Pro iQ Plus instruments). Calibrated up to 1000 m/z.
Unit: 0.7 Da
Wide: 1.2 Da
Widest: 2.5 Da
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. 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. If this value is Ramp, see Advanced Acquire > Ramp Table.
Fragmentor ramp? – Whether or not to use the Fragmentor ramp for this scan. If selected, click to see the Advanced Acquire > Ramp Table. 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.
This toolbar is available for both Scan and SIM rows in the Acquisition Parameters table.
Toolbar icon | Action |
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![]() | 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. |
![]() | Moves the selected row(s) to the Fraction Collection Trigger Signals table. |
This shortcut menu is available when you right-click a number parameter in this pane.
Deletes the current contents. This command is only available when you select the contents of the current parameter.
Copies the current contents. This command is only available when you select the contents of the current parameter.
Pastes the contents from the Clipboard into the current location
When selected, 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. Consider the peak width that results from the chromatographic conditions when setting the Targeted points per second (Hz).
When you clear Targeted points per second (Hz), enter the desired value for Scan/Dwell time (ms) for all Scan types.
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. 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.
If a method has only SIM scan types, the Actual targeted points per second will list only the closest value to the Targeted points per second value entered by the user.
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.
The Estimated cycle time and the scan speed are estimates.The Fraction Collection Trigger Signals table is available only if a fraction collector is configured and connected and you are running OpenLab CDS 2.8 Feature Pack 02 or greater.If no fraction collection trigger signals are enabled, the following occurs:All fraction collection trigger signal data will be acquired by the MS as specified in the sequence and the method Fraction collection trigger signals table.All fraction collection trigger signals will be acquired just as they would be if the MS signals were enabled for fraction collection and will be seen in Data Analysis.No fractions will be triggered based on MS signals, and no fraction trigger start and end marks will be down on the mass-based fraction collection traces in Data Analysis.UV fractions will be triggered based only on the UV signal and according to the fraction collection settings for the UV signal.To trigger fractions based on these MBFC signals, the peak trigger used in the SQ method must be enabled in the fraction collector. Data for MS peak trigger signals that are not enabled can be viewed in data analysis and fraction preview, but they will not trigger fraction collection. |
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.
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.
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 Targeted points per second (Hz), 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.
The percentage of each cycle that is used for SIM. Use SIM % to adjust the duty cycle of the instrument between SIM data acquisition and Scan data acquisition as appropriate for your workflow. Scan mode performance may be improved with a lower SIM % due to improved sampling of ions. Longer scanning typically results in improved sampling. For example, a SIM % of 5% would be appropriate for a method with two Scans and three SIMs.
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. 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 clear and then select Targeted points per second (Hz).
If the method does not have any SIM segments, then the SIM % parameter is not available.
Use the Fraction Collection Trigger Signals table to specify the adduct ions in the single ion monitoring (SIM) mode to be used as the fraction collection peak trigger signal for a compound. The peak trigger signal for a compound is the sum of all the SIMs for the compound that are assigned to the same Fraction collector peak trigger. This includes both positive and negative polarity adducts.
The Fraction Collection Trigger Signals table is available only if a fraction collector is configured and connected and you are running OpenLab CDS 2.8 Feature Pack 02 or greater.If no fraction collection trigger signals are enabled, the following occurs:All fraction collection trigger signal data will be acquired by the MS as specified in the sequence and the method Fraction collection trigger signals table.All fraction collection trigger signals will be acquired just as they would be if the MS signals were enabled for fraction collection and will be seen in Data Analysis.No fractions will be triggered based on MS signals, and no fraction trigger start and end marks will be down on the mass-based fraction collection traces in Data Analysis.UV fractions will be triggered based only on the UV signal and according to the fraction collection settings for the UV signal.To trigger fractions based on these MBFC signals, the peak trigger used in the SQ method must be enabled in the fraction collector. Data for MS peak trigger signals that are not enabled can be viewed in data analysis and fraction preview, but they will not trigger fraction collection. |
If no fraction collection trigger signals are enabled, the following occurs:All fraction collection trigger signal data will be acquired by the MS as specified in the sequence and the method Fraction collection trigger signals table.All fraction collection trigger signals will be acquired just as they would be if the MS signals were enabled for fraction collection and will be seen in Data Analysis.No fractions will be triggered based on MS signals, and no fraction trigger start and end marks will be down on the mass-based fraction collection traces in Data Analysis.UV fractions will be triggered based only on the UV signal and according to the fraction collection settings for the UV signal.To trigger fractions based on these MBFC signals, the peak trigger used in the SQ method must be enabled in the fraction collector. Data for MS peak trigger signals that are not enabled can be viewed in data analysis and fraction preview, but they will not trigger fraction collection. |
Click a column header to sort the table by the 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.
The following information is available in the Fraction collection trigger signals table.
Compound name – The name of the compound.
Fraction target mass column – The fraction target mass method override column to use in sequences. The compound name, compound formula, and monoisotopic mass specified in the sequence table will override the values specified in the method, and the m/z for the adducts will be calculated based on the compound values from the sequence.
Fraction collector peak trigger – The MS peak trigger with the peak detection settings to use for triggering fraction collection for the compound. The peak trigger is defined and enabled in the fraction collector method, where you set the peak trigger slope, threshold, and all other peak trigger parameters.
To trigger fractions based on these MBFC signals, the peak trigger used in the SQ method must be enabled in the fraction collector. Data for MS peak trigger signals that are not enabled can be viewed in data analysis and fraction preview, but they will not trigger fraction collection. |
Compound formula – The formula for the compound. If the formula is present, it is used to calculate the monoisotopic mass. If the formula is empty, enter a monoisotopic mass.
Monoisotopic mass – The monoisotopic mass of the compound. This is based on the formula or can be entered in place of the compound formula. It is used to calculate the m/z used for the SIM signal for each adduct.
In the case of a multiply charged adduct, the monoisotopic mass can be outside the mass range of the MS as long as the resulting adduct m/z is within the instrument's mass range.
Two different rows in the table with the same compound name but different monoisotopic masses are not allowed.
Adduct species – Value is based on the selections in the Adducts pane in the Edit compound window. See Edit the Mass-based fraction collection table.
Polarity – Value is based on the selections in the Adducts pane in the Edit compound window. See Edit the Mass-based fraction collection table.
m/z – Value is based on the Ion Species formula and monoisotopic mass, and cannot be edited.
Quad res – Select the option for the quadrupole resolution to control the mass window and peak width. This value is only available if the Scan type is SIM.
Narrow: 0.4 Da (available only for Pro iQ and Pro iQ Plus instruments). Calibrated up to 1000 m/z.
Unit: 0.7 Da
Wide: 1.2 Da
Widest: 2.5 Da
Dwell time (ms) – This calculation is based on the Targeted points per second, mass range, and SIM %. The value is editable if Targeted points per second is not enabled in the Acquisition Parameters pane.
Detector gain factor – See Detector Gain Factor. 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. If this value is Ramp, see Advanced Acquire > Ramp Table. Fragmentor value cannot be ramped for SIM signals used as Fraction Collection Trigger Signals parameters.
Toolbar icon | Action |
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![]() | Expands all compounds in the table. |
![]() | Collapses all compounds in the table. |
![]() | For editable columns, fills all cells in the column with the same values as the selected cell. |
![]() | Cuts the selected row or compound from the table and adds it to your clipboard. |
![]() | Copies all the adducts in the compound for a select compound row. For each adduct copied, the compound information is prepended to each adduct row. |
![]() | Pastes the cut or copied row or compound from the clipboard. Selecting a compound row copies all the adducts in the compound in the form of one row for each adduct with the columns for both compounds and adducts. Individually selected adduct rows are copied and the corresponding compound information is included for each selected adduct. |
![]() | Moves the selected row(s) to the Acquisition Parameters table. |
![]() | Opens the Add compound dialog. |
![]() | Opens the Edit compound dialog. |
Advanced Acquire > MS Global Parameters Pane
Advanced Acquire > Chromatograms
Edit the Acquisition Parameters table (LC/MS)
Add or edit compounds in the Fraction collection trigger signals table (LC/MS)