Category Archives: General Use
Quan Peaks, Confirming Peaks and the mysterious Mass Filter
In TraceFinder, the lowest form of identification is the peak, but the lowest form of data aggregation is the compound.
Unlike Xcalibur and LCquan, where each individual trace is a component or associated with a single component, TraceFinder allows for the compound to consist of up to 6 quan components. Each of these components CAN, but does not require, be associated withup to 10 confirming peaks.
Each Confirming Peak is assigned a ratio to the associated quan peak. The relation ship of a Quan to a Confirming lies in that they must exist at the same point in time, thereby they must co-elute chromatographically. Also they must exist in a specified or calculated abundance to each other.
Again, unlike Xcalibur and other apps from Thermo, these two peaks do not have to exist in the same Mass Filter. The Mass Filter is a designation in the data file that narrows down where to recover the Time and Intensity pairs of data that represents the abundance of an ion at a particular point in time. This is what is used to construct the 2-D chromatographic plot.
This means that in a SIM experiment a quan peak can be select from one mass filter and the confirming ion can be from another. In an SRM experiment the quan peak could theoretically be from a positive precursor-product filter and the confirming could be from a negative precursor-product filter. In a Full Scan High Resolution Scan experiment,as from an Exactive type instrument, a Quan peak can be selected from a full scan and the confirming peak can be selected from a HCD or AIF scan. By utilizing this technique with no calibrators samples in a batch of samples a chemist can conduct a screening assay for the present/not present answer set.
The next unique quality of this flexible designation is that multiple quan peaks can be selected for a compound and be from separate filters and at different retention times. this would allow for multiple peaks to throughout the chromatographic assay to represent the total response of a compound. This would be best illustrated by compounds that use chiral separations, where one isomer would elute faster than another but the response of both need to be summed as the total response for the calibration curve and amount calculations. By utilizing this feature there is no exporting of results grids to excel or a LIMS system just to calculate the total compound.
Brief description of flagging colors
NO Flag – Criteria for flagging on a compound was not met or flagging criteria was defaulted as off by being set to zero. No criteria or no level beyond the set threshold, No flag
Green Flag – Certain compounds, such as those designated as internal standards have default criteria that is not defaulted as off. Green flag means all the criteria is meet.
Yellow Flag – A compound did not have a peak defined peak detected as a quan peak.
Orange Flag – Used to designate that a value of the calculated amount lies between the LOD and The LOQ as set in the QC/Limits section of the master/local method.
Red Flag – Used to designate the failure of a set limit in the QAQC/Limits section of the master/local method, including threshold failures, ratio failures, etc..
How to Create a Master Method and Batch From DrugX
This attachment breifly describes how to make a batch with already acquired data using drugx demo data from the xcaliburexamples folder
Creating a Master Method from an Xcalibur PMD file
Here’s a quick way to turn your old xcalibur processing methods into TraceFinder Methods.
Click on the link to a word docx file below
Ion Ratio Settings and the uneditable percent
In TraceFinder under the General Tab you can set select:
- Manual – typed in and manual adjusted for each confirming peak
- Average – calculates the average of the ratios across the calibration curve and uses that as the percent entry for the ratio
- Weighted Average – calculates the average of the ratios across the calibration curve with a weighting and uses that as the percent entry for the ratio
- Level – Uses a level that the use selects for calcualtion of the ratio
IF the user selects anything other manual, those values are not editable.
If the Curve or the level have not been completed, then with all other selections results for the samples before either the last calibration sample or the selected level will not have a ratio defined to flag against.
Video For manual and other settings for ion range calculation
