Category Archives: Tutorial

A tutorial on how to setup and process High Resolution Accurate Mass (HRAM) screening and quantitation data sets in TraceFinder 4.1 

FreeStyle tutorial: Automated Peak Detection settings

The video below demonstrates how to setup automated peak detection settings inside of a workspace, through annotated click-through text.

Freestyle tutorial: Comparing Chromatograms

The video below demonstrates how to compare chromatograms in a workplace, through annotated click-through text.

FreeStyle tutorial: Background Subtraction

The video below demonstrates how to perform background subtraction, through annotated click-through text.

FreeStyle tutorial: Elemental Composition

The video below demonstrates how to determine the elemental composition of a spectral peak, through annotated click-through text.

FreeStyle tutorial: Displaying Mass Spectra

The video below demonstrates how to mass spectra inside of a workspace, through annotated click-through text.

FreeStyle tutorial: Averaging Spectra

The video below demonstrates how to average mass spectra inside of a workspace, through annotated click-through text.

FreeStyle tutorial: mzVault Searches

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

Issues with Actively Scanning Virus Protection Applications and Data Acquisition and Processing

In many instances of instrument and processing stations being connected to the internet, I’ve helped individuals having system lock up issues on various mass spec systems over the past 20 years, when using Real-Time Virus Scanning Protection.

This issue is vendor agnostic and will causes problems in data collection and processing on a number of vendor platforms.

If you have Norton, McAfee, Microsoft Security Essentials/Windows Defender, etc and you need to run real-time virus protection. You should exclude the folders where data is actively being collected and processed. This will ensure that any processes, such as instrument communication, raw data writing to disk or processed result file creation,aren’t being interrupted by virus checking during data collection and manipulation.

Below is a list of folders recommended for exclusion in the various anti-virus programs.

The example comes from Windows Defender in Windows 10, and will have a different user interface dependent on what application you are using, however each application available commercially today has this capability.

1:Real-time protection is on and select settings

Capture2

2: Select Add an Exclusion

Capture3

3: Add each of these folders as an exclusion

Capture4

New Confirmation Setting in TraceFinder 4.0 and above

TraceFinder has always had a plethora of criteria that is available to assist in the review of data quality. Below is a picture of the Chromatographic Suitability panel that can be set for each peak individually or as a global setting. This flagging criteria has existed since Xcalibur’s creation in 1994. However, unlike Xcalibur, TraceFinder will report out the actual measured value of each set criteria versus the simple PASS or FAIL. These values can be visualized in the data review summary flags or utilized in creating reports.

However, on each type of confirming criteria (Ion Ratios, Isotope Patterns, Library Searches, etc..) there exist the ability to turn them on or off for the method. Added in the TF 4.0 release is the ability to enable the Required option. Setting this option allows the users to control for peaks that only pass the set criteria. All peaks that have the Required option turned on for one or many confirming criteria and have a failed value for the Required option will not be intergrated. Thus, it will be as if the peak was not found in the sample.

This is an optional feature and is turned off by default when the compounds/peaks are created in the Master Method Template.

capture