Blog Archives
Freestyle tutorial: Comparing Chromatograms
The video below demonstrates how to compare chromatograms in a workplace, through annotated click-through text.
FreeStyle tutorial: Background Subtraction
The video below demonstrates how to perform background subtraction, through annotated click-through text.
TraceFinder 3.2 – Method Setup Tweak – Threshold Setting
There have been a few questions on the issue of peaks not being integrated, while performing quantitation, although the signal is strong. A reason could be that when a compound is created in the method, it has a related compound database entry for a threshold setting. This setting is used in targeted screening but is not editable in quantitation mode.
The setting has a default value of 5000 for calculated peak area. This setting does have a global override in the Local and Master method Processing section. The default value is unchecked and blank. This means the default threshold is 5000 for all peaks. If you are having an issue where the peak is not integrated but has a strong signal, then change the setting by checking the box and entering a new value such as 0 or 500. The data will need to be reprocessed as this value is not automatically applied.
Thermo Freestyle – Data Dependant Navigation Tutorial
In the pending TraceFinder 3.2 release, FreeStyle will be an optional feature that comes with every installation.
FreeStyle is a new qualitative viewing package that is taking on the features of QualBrowser.
TraceFinder 3.2 gives you the ability to utilize both QualBrowser and Freestyle when analyzing data, from links within the application.
Please view the video below as a quick tutorial on the data dependant navigation of FreeStyle.
Video player has changed. If the picture appears blurry, in the top right hand corner of the player you can enable HD to play back high resolution video.
Thermo FreeStyle – Sequence Navigation tutorial
In the pending TraceFinder 3.2 release, FreeStyle will be an optional feature that comes with every installation.
FreeStyle is a new qualitative viewing package that is taking on the features of QualBrowser.
TraceFinder 3.2 gives you the ability to utilize both QualBrowser and Freestyle when analyzing data, from links within the application.
Please view the video below as a quick tutorial on the sequence navigation of FreeStyle.
Video player has changed. If the picture appears blurry, in the top right hand corner of the player you can enable HD to play back high resolution video.
Thermo Freestyle – General Navigation Tutorial
In the pending TraceFinder 3.2 release, FreeStyle will be an optional feature that comes with every installation.
FreeStyle is a new qualitative viewing package that is taking on the features of QualBrowser.
TraceFinder 3.2 gives you the ability to utilize both QualBrowser and Freestyle when analyzing data, from links within the application.
Please view the video below as a quick tutorial on the basic navigation of FreeStyle.
Video player has changed. If the picture appears blurry, in the top right hand corner of the player you can enable HD to play back high resolution video.
Note: FreeStyle is a separate application and will require a separate license from TraceFinder.
However, when you apply for a TraceFinder 3.2 license you will receive both a TF license and a FreeStyle license.
You simply apply each to their respective license when using the applications together.
Sneak Peek – Targeted Screening
As Always the TF team is looking forward and addressing market driven issues.
One thing that has become highly vocal in the applied markets is the ability to screen for target molecules, and then quantitatate on the positive hits.
So in a forth coming release, TF has incorporated the ExactFinder Screening workflow into its core set of capabilities.
We’ve expanded on this, to include nominal mass instruments, as well as, the high resolution accurate mass systems. This will allow for us to screen utilize screening from the single quandrupoles all the way to up to the QExactive.
So below is a shot of the new screening data review, and you can get an idea of the new UI style adopted by Thermo Scientific.
We still will have the same quan workflow, but have added acquistion and realtime reporting to ExactFinder screening workflow.
Now that I have a CDS, what do I do with it?
Well, the end game of the CDS is to supply information that can be used to create methods and acquire data.
Here we’ll look at the Acquisition List side of the equation.
Here in the data we retrieved from a CDS or PMD file is stored.
Note that PMD files do not contain all instrument information but this can be added to a CDS and then adjusted.
From here you can select the export SRM data in the Method View tab and an Xml file containing the instrument specific data will be produced.
If you open this file in a text editor such as note pad it will contain the information in the Acquisition List in a format that can be imported into the Instrument Method editor.
If on the Batch View section or the final page of the Acquisition Mode wizard you select Auto-TSRM update this information is passed to the mass spec at the time of acquisition. This allows the user to collect only the data needed to be processed and allows for manual updates in the batch to be automatically loaded to the mass spec at run time. This does not monitor the RT of peaks and automatically update the mass spec controller, but allows for user input to occur in on place versus having to open the instrument editor for a second adjustment.
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.
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.
TraceFinder: Direct Knowledge 