Tip!
To edit an existing processing method, click
Process Method > Edit embedded method
and
then use the following steps.
3. Select the Workflow page and then select at least one workflow and the reference samples.
4. Select the Components page and then define the component names, masses, internal standards, groups, and
so on.
Tip!
If the group is defined in the Components table, then the user can choose to sum the ions in the group,
even if the precursor ion and the experimental index are different for the transitions. The summed ions are
not shown in the table but are shown on the Integration page and in the Results Table as <group name>_Sum.
This feature is useful for the quantitation of proteins and peptides.
Tip!
Where the retention time of the components is not known, set the
Retention Time Mode
for a
mass or chemical formula to
Find n peaks
, where
n
is 1, 2, 5, 10, or all. The software identifies the specified
number of features with the greatest peak area, assigns the appropriate retention time, and then performs
a targeted peak processing workflow. When processing is complete, the embedded method for the Results
Table can be saved as a normal targeted method.
5. Select the Integration page and then select the integration parameters for each component.
6. Select the LibrarySearch (workflow-dependent) page and then define the library search parameters.
7. Select the Acceptance Criteria page and then select the acceptance criteria for peak integration, accuracy of
standards and quality controls, and the calculated concentration range for the unknown samples.
8. Select the Qualitative Rules (Confidence Limit) page and then define the traffic light settings for mass accuracy,
retention time difference, isotope match, library score, and formula finder score.
9. Select the Ion Ratio (Confidence Limit) page and then define the traffic light settings for the ion ratio acceptance.
Ion ratio is the peak response ratio (area or height of qualifier and quantifier).
10. Select the Formula Finder page and then select the formula finder settings.
11. Select the Non-targeted Peaks page (only available when the Non-targeted workflow is selected) and then
define the Non-targeted search parameters.
12. Click
Save
.
Tip!
When a Non-targeted method is created, the current project default parameters are used for peak
integration, and those parameters are saved in the method file. If the processing method contains the targeted
analytes, then the customized integration parameters for the targeted components will not affect the
Non-targeted peak integration. If the user changes the project default parameter later, then the changed
parameter will not impact the existing Non-targeted method, which still contains the parameters at the time
the method was created. Only the newly created non-targeted method use the changed parameters.
SCIEX X500 QTOF System
System User Guide
149 / 234
RUO-IDV-05-2334-E
Operating Instructions—Software
