Blog Archives

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.

Back After A Long Holiday – Inheriting ExactFinder in TraceFinder 3.0

Below is an application note for ExactFinder, that deals with Targeted Screening.

This capability has now been moved into TF 3.0, so going forward those who have EF will be able to do the same functionality.

On the Plus side is that you can do it with a system that acquires and processes on the fly, versus batch processing. This will give you real time analysis and lets you see data/reports soon as the sample is done. NO WAITING.

Also with this capability and the export functions in the data review grid, there is an enhanced method development workflow that has been mapped out, which we will discuss in a later blog.

Link to PDF of Poster:




New Look and Feel for the Compound Database in TF 3.0

When TraceFinder originally launched we introduced the concept of using a compound data base for storing compound information for use later in method development.

Over the last couple of years we’ve found that more information was needed for use in some complex experiments that were becoming more common.

So we had several discussions with customers, on how to make this an easier process to get data in and alter it once it was in.

In TraceFinder 3.0 you will find a completely new user interface for the CDB. It allows for a detailed view and editing of data needed for Quantitative and Targeted Screening experiments. More ease of use features are yet to come but if you were a user in the past, you should find this interface quite a bit simpler to use.

We have also incorporated the ability to export all the data to Excel for grid type editing and then reimport the changes.

If you have compound data stores from legacy versions of TraceFinder or compound data bases from ExactFinder, simply choose the file and import it. TraceFinder converts and validates the data into the TF 3.0 format.

You can get an overview of the CDB in 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.

New TF 3.0 Targeted Screening Workflow in Data Review (or the marriage of TF and ExactFinder)

A new feature to TraceFinder 3.0 is targeted screening. The workflow and method setup that were included in ExactFinder has been included in TraceFinder 3.0. Though it has been expanded to support Nominal Mass as well as HRAM.

That means this feature will work for all mass spectrometers from the GC single quads to the Q-Exactive.

Though some sections are more geared for HRAM, they can just not be used when using nominal mass data.

The other aspect is that TF gives you the ability to acquire, process and report on the fly during acquisition. Therefore, if you so choose you don’t have to wait to review your data. So this expands the capabilities that was introduced in ExactFinder.

This is our first step with this functionality and more is to come in following releases, but there are some interesting things that can be done by having these two workflows combined.

Again the video is a little longer that my 2 minute rule but there is a lot to look forward to.

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

Need to just enter some compound info for the method… Ok here’s a solution

So at times we’ve had the request that chemist just want to enter in some compound data without having a rawfile to extract the spectra from.

And though TF gives you multiple ways of creating methods, some feel they just want to be able to add a compound and input their data by hand.

Though many workflows support doing this in using a CSV file and creating a method from importing that csv file into the CDS, sometimes that just may be too much.

So here is couple of CDS files that you can have on hand just to pull over and fill in place holder information.

One is for XIC/SIM type of experiments and the other is for SRM type of experiments.

Making changes in to the multiple peaks in a compound (Answer to a “Ask A Guru” question)

There are times that a chemist may make a method from a PMD file or from CDS, and things need to be changed.

An istance would be swapping an existing quan peak with its confirming peak, or removing a confirming peak.

These changes while seemingly trivial can be a hassel if you have to do many of them. So the TF team has given these options as right click contect menus to make it easier to perfrom these functions.

Watch the video below to get an idea of how to use these tools.

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

Compound Data Store or Compound Database – Kinda the same thing….

TF has the concept of bring in a data you know about compounds and storing it for later use.

This we call the Compound Data Store (CDS), but what’s in a name… Its a an XML file that contains information about the compound.

The picture above shows this data in excel. It contains information like the compound name, experiment type, collicion energy, retention time, fragments relationships.

Attached here is a copy of the csv template TEMPLATE.

This information can be edited in excel and uploaded into TF to add to a database or to alter the data base. The changes will be reflected in the TF CDS module.

Once the data is in the CDS, a method developer can utilize it to create processing methods which in turn can be used in syncing acquistion methods in the Master Method.

A blog post to come later this week will highlight the use of the information in the Auto-SRM feature.

A quick note is that the CDS is not automatically turned on at installation.

The user will have to configure the option and restart TF to take advantage of this feature.