Category Archives: Method Development

TraceFinder 3.2 – Intelligent Sequencing as a Standard Feature

TraceFinder 3.2 will include Intelligent Sequencing as part of the standard features set.

Previously, this was an additional add-on to the TF applications, with a separate license.

Now Intelligent Sequencing will be able to be configured in the Application Configuration section of TF, as shown below.

If you are not familiar with Intelligent Sequencing, it is the capability to perform actions on the sequence list of samples from real-time analysis of the flagging system.

The uses of this feature are numerous, the main benefit is that you have a safeguard for your samples.

– If you have a QC sample that is out of tolerance, you can stop the acquisition of following samples.

– If you have carryover in your blank, the system can automatically introduce additional blanks until it is clear or stop the sequence after so many blanks have been injected.


App Configuration



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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Peptide Quantitative Method Development with TF3.1

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.

My Filter String Is Missing After I Updated My Methods Associated Rawfile.. HMMMMMM

So in both the local and master methods, a user can update the associated rawfile to see the peaks they are looking for.

This dialog has an option to update the filter strings. Which makes it easy to do especially if you have hundereds of compounds.

Associate rawfile

When you do this, the logic looks to the compound database info that is in the Acquisition list and to help it determine the filter with the right precusor and then the extracted ion setting to see which filter contains its value within the range of product ions in the brakets of the mass filter. If everything matches from the newly selected rawfile it sets the filter accordingly. If it doesn’t then the compound will have a little red dot next to its name and a missing filter error lights up.

This typically occurs when the new file has a slightly different filter string and the method’s extracted mass falls outside of the product mass range of the filter.

The following video shows you how to manually fix this issue.

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 – 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.

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.

TF 3.0 Converting Data from older versions for use in TF 3.0

In TF 3.0 there were alot of enhancements to how we handles the data. So we made sure that you can can seamlessly review your data created in previous versions.

Also all your templates and methods can be converted.

The Legacy Data Converter allows for browsing to all stored data locations and can replicate the original folder structure to fit within the TF 3.0 framework. Once converted you will be able to browse, review and report any of your old data in TF 3.0, but the original results and files remain in their locations so that the batches, method and templates are never destroyed.

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

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.