Category Archives: Special Calcualtions

Residuals Chart Report Template

In many instances, individuals wish to see the residual values of their calibration curves. This plotted chart may give a better visualization of how the curve is actually performing versus the singular R-squared value.

Click here to download the report templates for data that contains either internal or external standard curve types: Residual Chart Reports

Extract the files to the file location: C:\TraceFinderData\4.0\Templates\ReportTemplates

For use with TraceFinder 4.0 and later versions.

Presented are charts in both natural and logrithmic scales. If you only require one type of chart, the delete the one not desired and resize to meet your needs.


The chart will automatically adjust for a normal amount of calibration standards or a large validation set.



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.

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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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.

How to do Background Subtraction w/ Qualbrowser

A couple of questions have come in, on how to best perform background or blank subtraction.

QualBrowser has a native tool to perform this task.

Please see the video below, on how to perform the operation on a single sample or a batch of samples using a .sld file.

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

TF3.0 – Using Estimated/Semi-Quan Amounts

In certain parts of TraceFinder and LabForms, we had exposed the ability to use estimated amounts of substances that did not have their own calibration curve. This feature goes back to the days of the Incos data systems, circa 1980.

In TF 3.0 we have exposed this capability, to be a bit more friendly to use and to be interactive in the user interface, versus just report generated.

In the following video, you will see where to set a compound to use the estimated feature and how it is displayed throughout the applications with visual clues to help you determine that the results you are observing is a semi-quantitative amount.

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.

Sneak Peek – Targeted Screening

As Always the TF team is looking forward and addressing market driven issues.

One thing that has become highly vocal in the applied markets is the ability to screen for target molecules, and then quantitatate on the positive hits.

So in a forth coming release, TF has incorporated the ExactFinder Screening workflow into its core set of capabilities.

We’ve expanded on this, to include nominal mass instruments, as well as, the high resolution accurate mass systems. This will allow for us to screen utilize screening from the single quandrupoles all the way to up to the QExactive.

So below is a shot of the new screening data review, and you can get an idea of the new UI style adopted by Thermo Scientific.

We still will have the same quan workflow, but have added acquistion and realtime reporting to ExactFinder screening workflow.


Matrix Spike and Matrix Spike Duplicate… Understanding the how it works.(Answer to a “Ask a Guru” question)

A question from the Ask a Guru was how to use MS/MSD samples and reports, well read below.

In the Environmental realm there is an experiment for a Matrix Spike and a duplicate, when compared to an unknown sample.

This allows for the chemist to calcualte a recovery of of the compounds contained in the unknown sample.

To set up the experiment the chemist needs three sample types.

  1. Matrix Spike – with compounds spiked into it at a known level
  2. Matrix Spike Duplicate –  with compounds spiked into it at the same level as the Matrix Spike
  3. Unknown – a sample with unknown amounts

Under QAQC tab of the Master/Local Method the concetrations of the spikes compounds must be entered in the grid for the MS and MSD tab.

In the Batch View the samples to be grouped together and used to report the Recovery must have the same SAMPLE ID. There must be one of each SAMPLE TYPE, but each one must have the sample SAMPLE  ID text in their individual grid cell.

When the batch is processed the data for recovery will be calcuated and a MS/MSD Report can be generated that displays the information about this experiment.

See the picture below of the report in Report View.

Thanks to Gail Harrison for her suggestion on a blog post.