Category Archives: Acquisition

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


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.

TF 3.0 – The Daily Technician Workflow – Point, Shoot and Read the report

Part of what makes TraceFinder a tool for the average chemist, is that complex experiments and processing can be setup once.

But then it can be used a thousand times, by technicians that just need to make samples and put them on the instruments to run.

Though there are many other things that can be done. Although, this isn’t an open access software, we have made it easy to just run your samples and get a report out on the fly that can go to a printer or to a pdf after each injection.

Please view 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.

Extending a Calibration Curve “Creating a historical cal file” – (Answer to an “Ask a Guru” question

One aspect of the applied market labs is that a calibration curve does not have to run with each batch of samples.

Previously we showed you how to associate the calibration file from one batch to the one you are currently working with.

In this video, we show you how to create a historical curve by extending a calibration curve from another batch.

By selecting the curve and the extend calibration function, the points found in the current batch of samples will be added to the points from the previously acquired batch of samples. This in conjuntion with turning on and off groups of compounds can allow for the user to build calibration curves for large sets of samples and use a historical running average of calibrators.

The video is from the soon to be release TF 3.0 but the workflow is the same.

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

Make it easy on yourself… Update in one place

In the Master Method you can review settings for your Triple Quad mass specs, such as Retention time, window of detection, collision energy…..

You can also make adjustments in the Master or Local Method to your Retention Time. Either by manual entry or by using several ways of performing automatic adjustments.

The issue comes in that when you make these adjustments in processing part of the method, the instrument method doesn’t know about them. So if you are using TSRM  you have to update in two places.

The Acquisition List is updated with the changes to windows and Retention times and can produce a file that can linked or exported out for adoption by the instrument method.

This allows you to edit in one place and by using the Auto TSRM update check box on the Acquisition section, You’ve just now reduced the typing and file coordination, that has to be done.

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

Method Forge … Acquisition and Method Creation

Below is a quick video of how to use the Method Forge feature while acquiring a data file.

Method Forge can be used with either an existing data file or be used to produce a data file using an instrument method. It then extracts the data out of the file and created compounds and components from detected peaks, defined in the assigned Method Template.

The Method template will be discussed in a post next week.

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

Quick Path to Data

Below is a short video on how to enter a batch using a template and begin to acquire.

At the beginning of  batch creation from a previously created template, containing the instrument method, processing method and desired reports.

Next you’ll see the ability to import a sample list from variety of file types and then submission of the batch.

Once submitted then user can watch the realtime trace of the collecting data segmented into a customized veiw  components and their order. While also having the capability to see the batch processing on the fly with a growing calibration curve and results.

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

Wizards and Batches… Removing the Warlock….

In TF there are three main choices to create batches. Each of these come from historical markets that TF is serving.

To start there is a selection of the type of creation you want to see. This is located in the Configuration mode under the Optional features section.

This allows the user to choose between the LabForms style wizard and the TraceFinder Acqustion Mode.

The TraceFinder Mode was made to make a wizard like workflow that naturally fit inside the application, and had a bit more intellegent checking of criteria before submitting a batch for Acqusition. This is the reason, that there are four mode buttons when it is enabled.

The Historical LabForms wizard was left in place to allow for users of that product to transition their existing workflow into the new application of TraceFinder.

Thereby, reducing the cost of the move. This view is more of a popup window and has some unique features. Eirther one allows for templates to be made and utilized in batch creation.

Finally Batches can just be made in a regular, non-templeted fashion by using the Batch View new batch selection.


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.

“Got Data?” – New Version on the way – TF 2.1

We are glad to announce that TraceFinder 2.1 is being cut to disks this week and will be on the shelves shortly.

The version has many “bug” fixes and performance improvements, but the BIGGEST feature is the ability to be run  on any detector Thermo supports. So if yo have a QExactive or a FID standalone GC, its supported. As well as, blended configurations.

So “Got Data?” we have a tool for you.

Plus soon to be published iBook for getting started with TF. “The Guru Guide”, written by the product manager for TraceFinder.

Remember if you have a question please fill out the form on the “Ask A Guru” tab. That message goes directly to the product manager or one of the support staff.