Blog Archives

Excel rules the world or at least it thinks it does…..

So, this week we’ve gotten a few questions on importing a sample list in CSV format.

There is an error that can occur if the csv file you exported and made adjustments to, is still open in Excel when you try to reimport it.

Unfortunately, the error message isn’t as descriptive as maybe it should have been, but it did give us a chance to post another answer to a “Ask A Guru” question

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.

Need To Look At Files With Data Dependant Experiments?

Though TraceFinder is primarily a quantitation application, it does have some provisions for unknown identification.

Mainly used in Single Quad or Ion Trap Analysis, the qualitative processing allows for scanning files along a TIC for peaks of interest and then eliminating the known targets and performing library searches against the unknown peaks. Also, TF gives the ability to look at the peaks that generate data dependant scans(DDS). It will sum the spectra and compare to a NIST style library.

To utilize this feature you must have two things. One a Method template, with the parameters set for Qualitative processing and DDS enabled, and a Sample Type of either and Unknown/TIC or Unknown Qual.

If you are performing Quantitative processing those will be perfromed first and Qualitative will occurs on the sample after Quan results are created.

If you have Qual resuts in data review you will have a green button to select the QualView.

Follow the the Video in setting up a Method Template and then using it in a Batch to review qualitative results.

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.

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.