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FreeStyle tutorial: Displaying Mass Spectra
The video below demonstrates how to mass spectra inside of a workspace, through annotated click-through text.
FreeStyle tutorial: Averaging Spectra
The video below demonstrates how to average mass spectra inside of a workspace, through annotated click-through text.
FreeStyle tutorial: mzVault Searches
The video below demonstrates how to perform mzVault library searches of spectra, through annotated click-through text.
Use FreeStyle to Create NIST 2014 Spectral Library Entries
TraceFinder 3.3 utilizes both the Thermo Library Manager and NIST 2014 HRAM library search system for confirmation and identification of found chromatographic peaks. To support the creation of HRAM libraries with NIST 2014 there are a few things to setup.
First, acquire NIST 2014 from a NIST distributor. Thermo has the rights to distribute via purchase this application. Also, FreeStyle 1.1SP1 will be needed.
Once installed there you must set up the spectra import default settings to match the decimal place criteria you plan on using for the type of data contained in your RAW file.
Next you must have Thermo FreeStyle 1.1SP1 installed.
Then you must set up two settings for data export to NIST.
Under the File menu, select File there is an OPTIONS button to click on. Then select Mass Precision and set the number of decimal places for the data type you will be using.
Next select the Library Search option and set the default to be MSMS or In-Source.
Save the settings. (Note: in some instances FreeStyle must be restarted for the settings to be implemented)
The next step in the process is to open the data file(s) you want to use to create library entries. Select the Workspace Processing selector and click the Library Manager button. Select the Library you want perform an initial search against. This must be done even if you are creating your own library.
This is followed by working up your data to reflect the spectra you wish to utilize and then clicking the Export to NIST button, while the spectra panel is highlighted. The NIST search panel will open and display an initial search result.
Next select the Librarian tab on the bottom of the screen and select edit button in the middle toolbar to open the editing panel; make adjustments such as changing the name of the spectra to be entered. Then select the Add to Library button finalize with the library file selection.
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 – 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.
Isotope Pattern Scoring in TF 3.1 – Answer to “Ask A Guru” Question
Below is an excerpt from the online help in TF 3.1.
A few questions have come up on how we calculate the isotope pattern score and visualization.
Here is the answer directly from the online documentation. Remember we do have comprehensive manuals and help under the Help Menu.
Link to PDF file: isotope scoring
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.
Need To Look At Files With Data Dependant Experiments?
Though TraceFinder is primarily a quantitation application, it does have some provisions for unknown identification.
Mainly used in Single Quad or Ion Trap Analysis, the qualitative processing allows for scanning files along a TIC for peaks of interest and then eliminating the known targets and performing library searches against the unknown peaks. Also, TF gives the ability to look at the peaks that generate data dependant scans(DDS). It will sum the spectra and compare to a NIST style library.
To utilize this feature you must have two things. One a Method template, with the parameters set for Qualitative processing and DDS enabled, and a Sample Type of either and Unknown/TIC or Unknown Qual.
If you are performing Quantitative processing those will be perfromed first and Qualitative will occurs on the sample after Quan results are created.
If you have Qual resuts in data review you will have a green button to select the QualView.
Follow the the Video in setting up a Method Template and then using it in a Batch to review qualitative results.
If the video is blurry select the cog wheel in the lower right of the video window and adjust the resolution setting.
Converting From Old to New… Methods, Data and Templates
TraceFinder provides an executable application the top level menu “Go” item, that will allow you to convert all of your old stuff to the latest versions of TraceFinder for use.
This includes all previous versions of TraceFinder and back to the LabForms 2.5.x application.
This allows you to reproduce your data and methods you currently use in the newer platform without having to recreate everything.
It also allows you to browse to any stored TF or LabForms directories to pull in the information even if, it has been archived on a remote disk.
After you have opened the directory the contents for the selected data type will be listed below.
You can select individual files or right click and select all. the simply press the “Start Converting” button in the lower right corner.
If any issues occur the Status column will contain an entry and the log file will record the issues with conversion.
TraceFinder: Direct Knowledge 