Parameters in the Optimization pane - TSQ Certis MS - TSQ Certis Tune Help - Parameters in the Optimization pane - Tune panes - Optimization pane - TSQ Certis MS

Injection Settings

Sample Injection Type

Infuse by Syringe or inject by Autosampler (automated with autosampler).

The Autosampler option is only available after you configure the autosampler in the Thermo Foundation Instrument Configuration, and reboot the system.

Optimization Options

Mass List Type

Select Precursor or Formula to define optimized compounds.

Polarity

Select the polarity mode (Positive or Negative).

• When the Mass List Type is set to Precursor, the options are "Positive" or "Negative".
• When the Mass List Type is set to Formula, the options are "Positive", "Negative", or "Both".
• If you select "Both", the MS evaluates precursors in positive and negative modes, and then uses the polarity with the most intense precursor for the product ion optimizations.

Positive Mode Adducts to Include

(Available when the Mass List Type is set to "Formula" and the Polarity is set to "Positive" or "Both".)

Select or define the positive mode adducts to include. For multiple adducts, the MS evaluates precursors with each adduct, and then uses the most intense adduct for the product ion optimizations.

You can select from the following options:

+H, +Na, +K, +NH4, and User Defined

Negative Mode Adducts to Include

(Available when the Mass List Type is set to "Formula" and the Polarity is set to "Negative" or "Both".)

Select or define the negative mode adducts to include. For multiple adducts, the MS evaluates precursors with each adduct, and then uses the most intense adduct for the product ion optimizations.

You can select from the following options:

-H, +CI, +OH, +HCOO, and User Defined

Spray Voltage Optimization

Select to optimize the spray voltage for the precursor ion. The MS uses the optimized value in the remainder of the optimization routine.

Default: Deselected

Adjust Start Voltage

(Available when Spray Voltage Optimization is selected.)

Select to input a start value for the spray voltage to use during spray voltage optimization of the precursor ion. The MS uses the optimized value in the remainder of the optimization routine.

Default: Deselected

Start Voltage

(Available when Adjust Start Voltage is selected.)

Specify the start voltage used for spray voltage optimization.

Range: 200–1,500

Source Fragmentation

Select to perform ion source CID energy optimization for the precursor. The MS uses the optimized value in the remainder of the optimization routine.

Default: Deselected

RF Lens (Precursor Ion)

Select to optimize the RF voltage of the RF lens for the precursor ion. The MS uses the optimized value in the remainder of the optimization routine.

Default: Deselected

Precursor Ion Mass

Select to optimize the precursor ion signal at the maximum of the measured profile peak m/z rather than at the theoretical peak m/z. The MS uses the optimized value in the remainder of the optimization routine.

Default: Deselected

Product Ion Optimization

Select to turn the Product Ion Optimization on or off.

• Off: The MS does not perform product ion optimizations.
• On: The MS performs product ion optimizations by using the properties defined in the Product Ion Optimization section.

Product Ion Type

Select whether for the product ions are known or unknown.

Default: Unknown

Number of Product Ions

Type the number of product ions to optimize. For known product ion optimization, define the m/z for the number of product ions defined. For unknown product ion optimization, the MS selects the most intense product ions.

Range: 0–10

Exclude Loss Mass (m/z)

Select the compound to exclude from the lost mass list. A "loss mass" is the precursor ion minus the defined loss mass (± m/z 0.9). The MS excludes these loss mass ions from being selected for optimization.

The available options are:

• H₂O, 18
• NH₃, 17
• CH₃, 15
• User Defined
• User Defined

Low Mass Exclusion (m/z)

Type the m/z value for the excluded mass. The MS excludes all the product ions below the defined low mass from being selected for optimization.

Range: 5–200

System Settings

Ion Source Settings

Select whether to apply the current ion source settings or the settings from the method with wash cycle.

• Currently Applied: Current ion source settings will be applied during compound optimization.
• From Method Template: Ion source settings from the method template will be applied during compound optimization.

Q1 Resolution (FWHM)

Select a Q1 resolution from the following options:

Range: 0.2, 0.4, 0.7, 1.2, and 2

Q3 Resolution (FWHM)

Select a Q3 resolution from the following options:

Range: 0.2, 0.4, 0.7, 1.2, and 2

CID Gas (mTorr)

Select a CID gas value from the following options:

0, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, and 4

Source Fragmentation

Specify the collision energy (in volts) for ion source fragmentation.

Range: 0–140

Data Folder

Specify the folder location for the report generation.

Default Path: C:\ProgramData\Thermo Scientific\Instruments\TNG\[Model]\[Version]\data\Optimization\

Buttons

Select Data Folder

Navigate to and select the data folder location.

Start

Starts the optimization routine.

Reset

Resets the parameters to the default settings.

Abort

Stops the optimization routine.

Open All Raw Files

(Available after an optimization routine is completed.)

Opens all completed raw files using the FreeStyle application.

Create Method

(Available after an optimization routine is completed.)

Creates a method based on the optimization input and the results of the user-selected compounds from the Optimization Results table and the optimized ion source parameters from the Source Optimization Results table. The method is saved as a .meth file in the user-specified location and can be opened using the Method Editor application.

Copy to Define Scan

(Available after an optimization routine is completed.)

Copies the selected row from the Optimization Results table to the Define Scan pane.

NOTE: The system allows copying only one row at a time; this button becomes inactive if multiple rows are selected in the Optimization Results table.

Copy to Ion Source

(Available after an optimization routine is completed.)

Copies the optimized spray voltage settings to the Ion Source pane.

NOTE: This button is inactive by default until you select a row in the Source Optimization Results table.

Back to Setup

(Available after an optimization routine is completed.)

Displays the setup options (Optimization Options, System Settings, and Optimization Table).

Display Results

(Available after an optimization routine is completed.)

Displays the results view (Acquisition Table, Optimization Results table, and Source Optimization Result table)

Clear

(Available after an optimization routine is completed.)

Clears the optimization results from the view.

NOTE: A PDF report is still available at the user-specified data folder location.