Category Archives: Tutorial

Issues with Actively Scanning Virus Protection Applications and Data Acquisition and Processing

In many instances of instrument and processing stations being connected to the internet, I’ve helped individuals having system lock up issues on various mass spec systems over the past 20 years, when using Real-Time Virus Scanning Protection.

This issue is vendor agnostic and will causes problems in data collection and processing on a number of vendor platforms.

If you have Norton, McAfee, Microsoft Security Essentials/Windows Defender, etc and you need to run real-time virus protection. You should exclude the folders where data is actively being collected and processed. This will ensure that any processes, such as instrument communication, raw data writing to disk or processed result file creation,aren’t being interrupted by virus checking during data collection and manipulation.

Below is a list of folders recommended for exclusion in the various anti-virus programs.

The example comes from Windows Defender in Windows 10, and will have a different user interface dependent on what application you are using, however each application available commercially today has this capability.

1:Real-time protection is on and select settings


2: Select Add an Exclusion


3: Add each of these folders as an exclusion


New Confirmation Setting in TraceFinder 4.0 and above

TraceFinder has always had a plethora of criteria that is available to assist in the review of data quality. Below is a picture of the Chromatographic Suitability panel that can be set for each peak individually or as a global setting. This flagging criteria has existed since Xcalibur’s creation in 1994. However, unlike Xcalibur, TraceFinder will report out the actual measured value of each set criteria versus the simple PASS or FAIL. These values can be visualized in the data review summary flags or utilized in creating reports.

However, on each type of confirming criteria (Ion Ratios, Isotope Patterns, Library Searches, etc..) there exist the ability to turn them on or off for the method. Added in the TF 4.0 release is the ability to enable the Required option. Setting this option allows the users to control for peaks that only pass the set criteria. All peaks that have the Required option turned on for one or many confirming criteria and have a failed value for the Required option will not be intergrated. Thus, it will be as if the peak was not found in the sample.

This is an optional feature and is turned off by default when the compounds/peaks are created in the Master Method Template.


Tip for Optimizing the Speed of Processing Data for TraceFinder 4.0 and later

TraceFinder 4.0 introduced the ability to perform target analysis on peptide sequences. Given that these chemical analysis methods can be very long (i.e. 3hours for a single sample) and have drastically shifting retention times between samples, TF 4.0 introduced the Extraction Time Window as a peak detection setting.

This new setting allows the user to set a window around where the peak might elute. The default setting is 3 minutes, which means +/- 1.5 minutes from the expected retention time.

This setting may be a bit wide for stable chromatography. A typical setting for the Extraction Time Window is 1 minute or +/- 30 seconds from the expected retention time. This setting can be changed in the Master Method Template or the Local Method.  This new setting can then be pushed to all the compounds with two mouse clicks or can be optimized for each target peak, clicking the Three Lined Button in the right coner of the settings page and selecting “Apply current extraction window settings to all peaks in the method

Since the amount of data being extracted for the targeted peak is reduced, the amount of time per peak analysis is reduced. This setting is separate from the Peak Detection and View Width Window under the Retention Times Tab.


Peak Extraction Window

Tips on Optimizing Speed for TraceFinder4.0 and later

The first tip for speed optimization can be used on any application. On many systems, the power setting is set for Balanced, especially for laptop users as this conserves battery power. However, graphic intense applictions and those applications that require your processor to be run optimally, need the CPU to be fully powered. Otherwise, the CPU and RAM will not perform at their specified speeds.

Under the Control Panel for Windows 7, select the High Performance Option.


High Performance Power Option


Second, Microsoft has put out a new version of the .NET Framework, which drives many of the underlying functions in Windows and applications written for Windows 7. Most people have no idea that this exist.

The new version .NET 4.6.2 fixes many issues Windows was experiencing with .NET 4.5.1, which TraceFinder 3.3 and above was installed with. Also, if your IT group or new PC has .NET 4.6 or 4.6.1, Microsoft has suggested that users install the new .NET 4.6.2.

Below is a link to download the framework from Microsoft. Please check with your IT group before making changes on a corporate PC.

.NET Framework Offline Installer

You can check your version of .NET Framework in the Control Panel/Add Remove Programs/Programs and Features


Add/Remove Programs .NET Version

TraceFinder Webinar series in Begins in October

please click the link below for more information.

Links to each webinar listed below:


Retention Time Reference Compounds Used For Correcting Chromtographic Drift

TraceFinder has an option to allow the user to set a reference compound to assist in corrections of retention time drift.

The feature is the same implementation that has been a part of the Xcalibur feature set for over 20 years and is well characterized. The user simply selects a checkbox in the RT Reference compound column of the Method – Identification tab. This sets the compound for use in linking other compounds to its found RT.

To set a compound to use a RT reference compound, simply select a RT Reference from a dropdown  selector in the same definition grid.

RT reference

The typical use of this feature is to set your Internal Standards as RT Reference Compounds and then link the nearby eluting components to the Reference Compound. Also, the IS retention time peak detection window is set a little larger than the target components to allow for detection if a large RT drift occurs.

When the RT reference is detected the difference, whether + or – in time are adjusted in the connected compounds. This new RT is specific to each compound in each sample. Therefore it is not reflected as a change in the method because the method is set as a batch level setting. The compound using the RT reference must have an original expected retention time to be adjusted, it cannot be left as zero for this feature to work.

Ion Ratios – How the range is calculated in the Methods, with added twist in TF 3.3

TraceFinder has 4 functions for ion range calculations.

Ion Range

1) Manual – This functions as the name implies, it allows the user to define a targeted ratio by manually entering it in the ratios section of the detection tab of the confirming ions of a compound.

2) Average – This functions allows the data to drive the targeted ratio of each confirming peak by averaging the detected peaks for each confirming ion in each component from the calibration curve and applying the average as the target ratio. This is useful in many clinical experiments where response may be variable across sample sets.

3) Weighted Average – Performs the same function as Average with the exception that it weights the bottom end of the curve in the calculation of the target amount. This is useful in assays where the expected amounts in the unknown sample types are typically on the lower end of the calibration range.

4) Level – This selection allows the user to select a level from the calibration curve as the target ratio reference. In some labs the SOP’s  require that a specific calibration point be compared for the batch of samples.

The selection of 2-4 are widely used in the applied markets. This relieves the use of having to perform the calculations manually outside of the application and then hand entering the data.

Also to note is that if you are working in a batch of samples such as a verification samples set. You may use settings 2-4 to calculate the values then changes the setting to manual. This action keeps the calculated value in the target field. you can then update the Master Method template and use these ratios for all validated batches to follow.

TraceFinder 3.3 has the benefit of being able to store the ion ratio criteria in the Compound Database so that you may perform quick holistic edits or use the same criteria in different assays without recalculating the values and manually entering them. As with the methods themselves, each ratio has properties that can be set as:

  • Window Type – How to calculate the width of the range around the target ratio
  • Ratio Window – The amount of the range
  • Coelution Value – The amount in time that the peak apex of the confirming ion can be different from the quan peak.


The file hyperlinked below is an example CSV file template for a compound database for TraceFinder 3.3. This file will allow you to record settings from other methods. If you are transferring from one instrument platform to another, this enables you to quickly create the same method in TraceFinder.

Click here to download the ZIP file -> Default

As a reminder TF can group in the CDB and the Method up to 6 components as individual integrated quantitative peaks under the compound name. This allows the peaks to be viewed and manually manipulated individually in data review but the responses summed as the total response of the compound. Each of the 6 quantitative peaks may have up to 10 confirming peaks with individual ratios and ranges.  (A key note is that the Quantitative peaks need NOT be coeluting. (ie.. Chiral compound analysis)) This feature is mostly when using GC EI experiments or LC experiments with multiply charged components.

TF 3.2 Setting up to Data Review to display Positive results first

In the video below, we have set up the flagging criteria to be able to sort and float Positive results, above the LOR/Cutoff Limit set in the method settings,to the top of the data review grid. We have also setup a flag to allow compounds with detected peaks but fall under the LOR/Cuttoff level in the QAQC section of the master/local method, to appear below the positive results. This should assist in labs wanting to review data by exception and to validate their data review process to incorporate into their SOPs to utilize this criteria.

TraceFinder 3.2 – New Quick Acquisition for Method Development

In previous versions of TraceFinder, there existed the Development Batch under the Method Development Mode of the application.

TraceFinder 3.2 has been replaced  with a new Quick Acquisition button in the toolbar and in the Tools menu items.

This allows the user to acquire a sequence of files and open them in either Qual Browser or FreeStyle, from any view or mode.

The main benefit is that the user can perform method development or simply acquire a file to test the system. This is done without having to utilize batch processing to get an quick answer to the question.

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 – 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.