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FreeStyle tutorial: mzVault Searches

The video below demonstrates how to perform mzVault library searches of spectra, through annotated click-through text.

Video – How to create NIST 2014 custom libraries with FreeStyle

To make custom libraries for use in TraceFinder 3.3 Unknown Analysis, the easiest way is to curate your spectra with FreeStyle and send to the NIST 2014 application which comes with the purchase of any NIST 2014 library.

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