Category Archives: TraceFinder 3.1

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


Troubleshooting – Windows 7 Themes Performance Issues

Change the theme to improve performance

If your computer is working slowly, you might see a message saying that the theme is using most of its allowed memory. If this happens, you can change to the Windows 7 Basic theme or a high-contrast theme to improve performance.

If you change the theme to Windows 7 Basic, you will no longer get the full Aero experience. Aero is the premium visual experience in this version of Windows. It features a transparent glass design, window animations, Aero Flip 3D, and live window previews.

To change the theme

  1. Open Personalization by clicking the Start button Picture of the Start button, and then clicking Control Panel. In the search box, type personalization, and then click Personalization.
  2. Under Basic and High Contrast Themes, click Windows 7 Basic or one of the High Contrast themes.

Issue with Column Arrangement in Data Review-How to Avoid and How to Fix

Some have experineced an issue when starting the application after rearranging columns in data review.

They recieve a .Net framework error that states that columns have been arranged to the left of frozen columns.

This is a known issue that will be fixed in the next version of TraceFinder.

To avoid the issue the columns in the image below should remain the farthest to the left on the data review grids.


If you experience the issue, rename the file tracefindersettings.sqlite to TraceFindersettings_old.sqlite and restart the application.

The factory default settings  backup file will be automatically recreate the tracefindersettings.sqlite file.

The image below shows the directory path to the file.

Note that the directory path is dependant on the version of TraceFinder that it is installed.


Xcalibur Quan Method to TraceFinder Methods for Quan Conversion

Below is a quick and simple way to move from Xcalibur based quan methods to TraceFinder.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.


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

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New In TraceFinder 3.1 – Sieve Unknown Screening Connector

TF 3.1 now includes a plugin kit, which allows for the rapid development of custom workflows within existing functionality of TF and external applications.

The first technology connection made is to Thermo Sieve 2.1.  This allows a user to send data to and receive selected results from Sieve. This gives TF the ability to complete the “Unknown to Known” workflow. This is accomplished by not reinventing unknown analysis inside of TF, but by leveraging the core competencies of TF and Sieve in a unified platform.

The video below is a short demo of how this works in an Unknown Analysis to Quantitative workflow, by Mark Sanders.

His accompanied ASMS poster is located on a previous posting.

Peptide Quantitative Method Development with TF3.1

The Power of Ease of Use – Is it TELEPATHY or TraceFinder 3.1? – Submitting a set of samples in realtime

Ya can get much easier in putting on a batch of samples to run, unless your telepathic.

Here is a set of sample just extracted and ready to run a method that was created for this bioanalytical assay.

The process is the same after the method development is done. It doesn’t matter if you are a GC, GCMS, LC or LCMS user.

It’s also no different whether you a clinical, environmental, food safety or just a general quan user. The power of TF is that it makes the technicians life, of data acquisition and review much easier.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

Method Development Unleashed – TF 3.1 and Multiple Instrument Methods

In an effort to help make TF a more friendly method development platform, we have introduced the ability to have an option to use multiple instrument methods in a batch of samples.

This ability is enabled simply by exposing the instrument method column in the sample definition grid.

When enabled the master method’s instrument selection is overridden, and the selected instrument method is used in its place.

This allows the user to have the same processing conditions but monitor the effects of chromatography differences on the peaks of interest.

Once an instrument method is optimized and chosen, simply turn off the column, update the Master Method and save.

All future batches of samples will use that instrument method.

See the video below.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

The Power of Comparing – Do these things go together? – TF 3.1: The NEW Comparative View in Data Review

Many have asked us, how to easily compare compound response across multiple samples.

Here is the answer.

Comparative View allows for a group of samples to be shown side by side with fixed Y-scale to the most intense or a selected threshold reference sample.

The view allows the user to visualize the Expected Retention Time and the Range of Time for peak detection via Markers. This will clearly indicate how the chromatography is responding.

The user can designate samples to be part of individual or multiple groups, by assigning alpha-numeric characters to column in the sample definition screen. Once assigned, and a member of the group is selected in the results grid, the multi-chromatogram pane will display the sample group in columns and the compounds in rows.

The use of a Threshold Sample and a new tab in the method under the Limits section, allows for a visual bar to be set for a specific peak height or a percentage of the Threshold Sample’s peak height.

Below is a video of the new feature in TraceFinder 3.1, debuting at ASMS 2013.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.