Category Archives: Data Review

Stop Bouncing Around When Reviewing Data

In Tracefinder you have the ability to review your data in the form of you final report in Report View.

By selecting the report you want to see and the data you want see it from, as long as its a Standard Report shipped with TraceFinder, you can see a preview of the report without actually creating the pdf or paper.

This is a virtual report help in memory while you review it. It allows the user to see the end result but still be able to make some changes.



A feature of many of the Standard reports that are sample centric is the Active View tab.

This tab allows the user to stay in the reporting area and make data review type changes. It will display the results found in the text of the report, but give you the ability to perform chromatographic editing just like in Data Review. Once all the changes are made then simply press an Update Report button that will appear above the virtual reports and the data on the report will be updated and the results in the Data Review Screen will be too.

This keeps you from clicking around from Report View and Data Review.

Enable/Disable Ion Ratio

In TF Methods Ion Ratios can be set but updated not to calculate if needed.

In this case the user may find that they have set up a sort of generic method with two confirming ions.

The body they are doing the work for requires only one as part of their data set.

The user can simply go to the method and select an ion and disable the calcualtion by unchecking the “Enable” box on the ratios page.

The ratio wont be calcualted and the chromatogram will not be displayed in data review or on reports.

Ion Ratios – Where are they Displayed

One question that has come up recently is “where are my measured ratios displayed?”

Well, Once you’ve processed your data, in Data Review of Analysis you can select a tab or display window to see Ion Ratios.

Below you can see the range of the accepted Ion Ratios as defined in the method, underlined in Red.

The Definition of what ion is measured, Underlined in Blue.

Finally, the actual measured ratio is circled in Red. If this value had fallen outside of the acceptable range then the peak itself would have a Red border around it.

The Sum of All Peaks

One of the key features of TF is the use of a compound being composed of multiple components.

So the gist, of it is that a specified compound can consist of up to 6 quantitative peaks, each of those can have up to 10 confirming ion ratio peaks.

So A compound can consist of up to 66 chromatographic peaks when using mass spectral data.

This means that you can visualize under the compound name quantitative peaks and their associated ion ratio confirming ions.


The compound is composed of these multiple peaks, which have summed areas. But they can be visualized separately. The total response of adding all the, lets say peak areas, is the total response of the compound. And by using the multiple quan peak feature, these chromatographic peaks don’t have to be at the same retention time. So if you were doing a chiral separation but wanted the total response, you would just make them individual quan peaks under the compound.


Now if you have coeluting peaks and want one big peak to represent your compound, then you can use the signal pane’s mass grid to accomplich this type of mass intergration.

All the responses are summed, but no individual visualizations.

Two ways in but no way out…… Xcalibur and TF open at the same time

HMMMMM…. Why am I golden but not green.. on my status ball.

All computer systems in the world, from a Operating System to specific applications like TraceFinder have a file managing system. Typically called an I/O or File I/O, for In and Out. This manages the handling of a file and the opening and closing of a file to extract data or other things inside the file.

Inherently TF and Xcalibur being from the same family of applications, act like siblings and try to grab the same file if they are both open at the same time.

If this happens then sometimes the door handle flies off and someone gets stuck inside.

When this occurs then rawfile will apprear as yellow status meaning it is acquired but not processed.

To fix this you just have to make sure xcalibur is shut down. and then proces the file. If for some reason that doesn’t work then you may have to reboot the PC. Not the best of situations, to say the least.

So Word To The Wise. Only use one Application at a time when Acquiring Data.

What the Heck is a Ion Range????????

So one thing that has been resurfacing is confirmations that I know what think is my data really is my data.

TF uses one such tool in Ion Ratio calcualtions.

This is a ratio of the selected response of one defined peak that is connected to another defined peak.

In TF, we define that as, a Confirming Ion has a Ratio to the Quan ION/Peak, and we can set some acceptance threshold around that ratio.

Now, we have a few ways of defining the Ratio.

Thats the Ion Range.

Now we can use:

Manual – Where you type in the Target Ratio.

Average – Where the Ratio is deteremined by Averaging the ratios found in the calibration curve for these peaks and then producing an average. This automatically sets the Target Ratio, so you don’t have to.

Weighted Average – The same as above but its weighted and usually used for really large orders of magnitude methods.

Level – Again its like the above but it only finds the Ratio for the one specified calibration level.

The last three allows the data to define your criteria, and keeps you from having to adjust the ratios manually. This can be done for processing on the fly or in post acquisition processing.

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

DrugX workflow tutorial