Category Archives: Uncategorized

Use FreeStyle to Create NIST 2014 Spectral Library Entries

TraceFinder 3.3 utilizes both the Thermo Library Manager and NIST 2014 HRAM library search system for confirmation and identification of found chromatographic peaks. To support the creation of HRAM libraries with NIST 2014 there are a few things to setup.

First, acquire NIST 2014 from a NIST distributor. Thermo has the rights to distribute via purchase this application. Also, FreeStyle 1.1SP1 will be needed.

Once installed there you must set up the spectra import default settings to match the decimal place criteria you plan on using for the type of data contained in your RAW file.

NIST import settings

Next you must have Thermo FreeStyle 1.1SP1 installed.

Then you must set up two settings for data export to NIST.

Under the File menu, select File there is an OPTIONS button to click on. Then select Mass Precision and set the number of decimal places for the data type you will be using.

Next select the Library Search option and set the default to be MSMS or In-Source.

Save the settings. (Note: in some instances FreeStyle must be restarted for the settings to be implemented)

FreeStyle Default settings

The next step in the process is to open the data file(s) you want to use to create library entries. Select the Workspace Processing selector and click the Library Manager button. Select the Library you want perform an initial search against. This must be done even if you are creating your own library.

Set NISt Library

This is followed by working up your data to reflect the spectra you wish to utilize and then clicking the Export to NIST button, while the spectra panel is highlighted. The NIST search panel will open and display an initial search result.


Next select the Librarian tab on the bottom of the screen and select edit button in the middle toolbar to open the editing panel; make adjustments such as changing the name of the spectra to be entered. Then select the Add to Library button finalize with the library file selection.

edit entry NIST

TraceFinder 3.3 – Targeted Quan Data Review – Simple Manual Intergation

There have been many request to ease the task of manual integration and other daily tasks in routine quantitation.

TF 3.3 utilizes the Swipe Integration and simple peak removal tools that were previously piloted in Comparative View. The data review elements have all been updated to give the review process a new look and feel. These updates allow for the data to be clearer and quicker for manual determinations.

As with Targeted Screening, TF 3.3 allows for the option to couple Unknown/Untargeted Screening with Quantitation to reveal components that were previously unknown for troubleshooting or determinations of new analytes, that need to be incorporated into future analysis. This feature is in the same previous workflows, but giving you the power to know more.

TraceFinder 3.3 – Targeted Screening Review

Targeted Screening has been a part of TF for several years now. However, in TraceFinder 3.3 the workflow has been coupled with Unknown/Untargeted Screening to allow the user quickly review chemical compounds that are thought to be present and to now include the ability to review components that are truly unknown. This allows the chemist to perform the same daily operations but know more than previously possible, in one simple workflow.

Tracefindr 3.3 – Create A Batch From a Template

TraceFinder 3.3 allows you to create templates to easily perform redundant tasks of everyday lab life.

By creating a batch template a user simply selects the template, enters the unique sample information for unknown sample types and submit the samples. The templates can be made to perform Targeted, Unknown or a Combination of analysis, dependent on the users requirements.

See a video below of this simple process that’s been around in TraceFinder for several years but now includes Untargeted Analysis when the option is available.

NEW – TraceFinder 3.3 including integrated Unknown Screening option

At ASMS 2015 TraceFinder 3.3 will be released. Though there have been many small improvements to the general Targeted Analyte workflows, there is now an option to perform unknown analysis as a stand alone or in combination with targeted analysis. When coupled with targeted analysis the Known Analytes are automatically removed from the found chromatographic peaks in the Untargeted list.

Quick points:

Identification of found chromatographic peaks include the options for use of:

  • Compound Databases used in targeted analysis
  • Library Searches (Both NIST 2014 HRAM and Library Manager 2.0)
  • Elemental Composition
  • Chemspider Searches

Below is a quick video of the major data review screens that can be utilized in examining your data.

What is Compound Discoverer?

What is Compound Discoverer?.

TraceFinder 3.2 – Infographic

easelly_visual (1)

New Video Download Page

We have gotten several request to have a download page for the videos posted on the site.

Some firewalls block the links to Youtube or th embedded video player.

Under the Tutorials Menu, we have added a Video Downloads page that contains a series of links to the major videos in the blog.

These links connect to a location that allows you to download the MP4 file. These may open up automaically in your browser or video player.

However they can be saved to disk from that application.

Video Download PAge

How to recreate the Heat Map Report in the new Report Generator.

Here’s another answer to a “Ask A Guru” question?

The Heat Map Report relies upon some advanced conditional formatting that isn’t supported by the current Report Generator. The new TEMPLATE editor looks like Excel, however it is a custom program. It’s conditional formatting is limited at the moment with more coming soon.

Even editing with Excel, some conditional formatting is not able to be executed when the report is generated.

However, you can generate the Simple Pivot Table Report in Excel format and then run a simple Macro to perform this function.

The video below walks you through how to set Excel to create macros, how to record a conditional formatting macro and how to create a button on the main toolbar, to be able to run the Macro with any generated report using the Simple Pivot Table feature.

How To Create a Simple Pivot Table Report And Add Customized Formatting In Excel

Below is an answer to an “Ask A Guru”, question.

The request was to learn how to set up a grid of samples in a row with the compounds as  columns and the calculated amounts as the data in the cells. Also to be able to format the report so that any amount that was not “0” or less to show blank in the cells.

To do this simply use the new report template generator and then edit the template format in Excel.  Since the report FORMAT not the data is stored in a .xlsx file the formatting in Excel stays when you save the file in Excel. Note that you must SAVE and NOT SAVE AS in Excel because the Template .xlsx file is linked to another file to render the results. If you SAVE AS and give it another name then the connection the other file is lost.

In this example the simple pivot table option was used to create the grid, and then Excel was used to format the fonts of the cells having zero or less for calculated amounts turn white. Thereby showing a blank cell in the grid for those cells containing the isolated values.

Video player has changed. If the picture appears blurry, in the top right hand corner of the player you can enable HD to play back high resolution video.