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.

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.

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.

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.


There Can Only Be One… Calibration Point

Even though its the most memorable line from the movie “Highlander”, this statement has come up many times for assays where semi quantitation occurs in screening analysis.

One way to accomplish a rough estimate calculated amount is to use the ability to use a single calibration level for a compound.

When you do this there are two settings in the Method setting that can be used.

Selecting Average RF allows for the average response factor for a calibration curve to be calcualted. If you use cal one point

the response of the point will be compared to the response of the compound in the sample and a rough estimate based on the

average will estimate the calcualted amount.

If using a linear curve and one point, you MUST set the Origin setting to Force. This sets the origin at Zero and draw the curve

the response of the one calibration point. Thereby giving you a curve to estimate the calcualted amount from.

There is a third way using Internal Standards, but we’ll save that for another day.

Method General Setting Page – Hmmm.. I missed that setting

One thing that TF has as part of its DNA is to be flexible. Method development is a complex process and we are always looking at ways to reduce the effort, but to give flexibility in our approach.

One page that has alot of power, but is over looked many times is the General Setting Page.

These settings are the general setting for properties in the method.

These settings overide the default settings in the Application and apply to the Method and consiquently all the data that is processed with the method. These settings can be changed in at both the Master and Local Method levels.

Two points to look at.

1) Mass precision – This applies to all the masses used in producing results. It does not apply to the reporting    properties of thethings like RT, or calcualted amounts.

2) Instrument Method Edit/Update – In the master method you have a copy of the selected instrument method, which the ultimate Master instrument method is located in the Xcaliber/Methods directory. When you select edit, you are editing the copy that is located in the Master Method folder. When you select update you are overwriting the changes you made in the Master Method Copy, to the ultimate Instrument Master method in the Xcaliber/Methods directory. When you use these button in the local method you edit the Local Method copy of the instrument method that was copied to the Local Method directory, and the update button copies those changes to the Master Method instrument method. This isolated the Ultimate Master instrument method from batch level changes that you may not want to be inherited by other Master Methods produced in the furture.

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.

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.



Converting From Old to New… Methods, Data and Templates

TraceFinder provides an executable application the top level menu “Go” item, that will allow you to convert all of your old stuff to the latest versions of TraceFinder for use.

This includes all previous versions of TraceFinder and back to the LabForms 2.5.x application.

This allows you to reproduce your data and methods you currently use in the newer platform without having to recreate everything.


It also allows you to browse to any stored TF or LabForms directories to pull in the information even if,  it has been archived on a remote disk.

After you have opened the directory the contents for the selected data type will be listed below.

You can select individual files or right click and select all. the simply press the “Start Converting” button in the lower right corner.

If any issues occur the Status column will contain an entry and the log file will record the issues with conversion.