Category Archives: Configuration

FreeStyle tutorial: Averaging Spectra

The video below demonstrates how to average mass spectra inside of a workspace, through annotated click-through text.

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

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.

TF 3.0 – What is Intelligent Sequencing? ” A new/old feature to increase reliability”

Intelligent Sequencing Control

The figure on the below illustrates the wide range of operator-defined
settings that may be utilized to allow TraceFinder 3.0 intelligent sequencing
to make real-time decisions that prevent manual review and re-analysis
of suspect samples. Data review is done immediately following
acquisition, and any defined actions can take place automatically
without user intervention.

Intel seque

Each of the key sample types – calibrators, quality controls,
specimens, etc. have their own review settings that can be unique
to a particular sample type.

For example, if a quality control does
not meet required QA/QC limits, the calibration can be completely
resubmitted and re-analyzed, effectively restarting the entire batch,
while a specimen not meeting that same QA/QC limit may only be
targeted for re-injection.

In each sample type, data review steps and defined actions can
be specified for acceptance criteria on data quality as outlined in the
laborotory’s SOP. The settings for these checks are shown in
the figure on the above.

Intelligent sequencing options can also be set
for quantitative values, such as limits of detection, blank cleaniness,
and carry over. Actions may be defined as well for review
steps based on ion ratio acceptance.

The benefit of utilizing this feature is that batches of samples can be run in realtime
with on the spot rejections or cleaning steps. This eliminates the need to return the
next morning and rerun samples. If samples have a short shelf life then they are kept from
having to be remade or running out of sample. Therefor, increasing the efficiency of the
lab and reducing waste of time and material.

TF 3.0 – How to add Adducts for use in the Compound Database

The video below shows how to edit the positive and negative adducts that can be used in the CDB.

The use of adducts becomes very useful in calcualtions of the exact masses for screening and high resolution quantitation.

This also helps in the screening qualitiy measurement of isotope confirmation and identification.

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

TF 3.0 to be released Monday Jan 28th. – Installation Guide

Here is the installation guide for TF 3.0

It covers how to install on a new system and how to upgrade currently existing systems.

Also the guide covers how to fill out and send in the registration codes to fully unlock TF 3.0.

TF 3.0 comes with a 120 day trial license, and will remind you each time you open the application to request a license.

The installation of “Power Modules” of Multiplexing Support and Intelligent Sequencing are covered under separate licenses, so they are requested separately from the main TF 3.0 process.

Link to TF 3.0 Installation Guide

TraceFinder 3.0 Installer

TF 3.0 uhhhh… Where did Configuration go?

TraceFinder has a few options that can be configured for use in the applications. These includes Power Modules which add significant functionality to default settings that a user has determined work best for them. Such as the use of PPM versus MMU for extracted mass range determination behind the scenes.


In previous versions the configuration mode was accessible in the main navigation panel, typically displayed on the left hand side of the screen.


It is now an always present COG wheel, in the upper right hand corner of the application screen.


So watch the video below to see how to access Configuration and what each section and specifically what some of the options do in and for the applications.


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


Intelligent Sequencing – Step One – Setting up the method

Intelligent Sequencing is not a new concept. In the late 90’s Thermo had an application called ToxLab which used the concept of flagging data and altering the sequence of the set of samples based on failure criteria.

This allows for insertion of blanks, reinjection of sample or a combination according to criteria that a chemist would normal use to look at his data the next day to determine, which if any samples had to be rerun.

Intel Seq just does this on the fly.

It allows the user to have confidence that the data will be handled in the prescribed manner using the existing on the fly criteria that has existed in TraceFinder for a number of years.

By using this feature the chemist can cut back time on reinjections and sometimes on sample prep since the sample wouldn’t have evaporated. Also it will not have gone beyond the sample stability time threshold before reinjection occurs.

The first part of the operation is setting flagging criteria as you have done previously.

The next is setting of the method criteria for Intel Sequencing.

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

Licensing….. How many licenses do I really need?

A question came across the Blog that asked about Licensing and Multiplexing?

The answer to the question is two.

One License for the version of the application(ie. TraceFinder EFS, TraceFinder Clinical, ect..) and One for the Additional Module such as Multiplexing support for the Aria OS.

IF you go to the upper left section of the application in the menu bar and select Help, at the bottom of the dropdown will be an item called License Activation.

Here you can open the licensing window and request or enter license data.

If your trial period is over then only a license screen will appear when you open the application from the file menu or from the desktop icon.

This is true for both the Application and the Additional Feature of Multiplexing.


Changes to My Method… Alot of them… Really?

So as a chemist sometimes it’s hard to believe that I didn’t make the perfect method.  Well, not really. Things change, cloumns go bad, my boss changed the SOP.

So considering the Master Method is my template used for creating batches with the same compounds and parameters, and it can hold up to 3000 compounds, which can have up to 66 components each, I don’t want to have to manually adjust each component.

In each section of the Compound detection tab there is a right click option that allows for copying of those settings to each component in the particular compound or across the entire method.

We hope this saves you time and lets you hit the weekend sooner so your not rerunning samples on a friday night.

If the video is blurry select the cog wheel in the lower right of the video window and adjust the resolution setting.