Free NIST Data Processing Software Lab for Universities - Part 4: Processing GCMS Data with AMDIS in Free Laboratory Resource for Universities

This series of instructional videos will introduce you to FREE resources for creating a gas chromatography-mass spectrometry (GC-MS) laboratory for college and graduate or even advanced high school level students. It could also be used as a self-study course. It demonstrates the power of electron ionization (EI) MS data obtained with GC-MS systems in the characterization of mixtures with computer library searches.

The NIST MS Search software and associated programs are utilized to process data and perform library searches. Two different chemical drawing programs can be employed to enter structures into the NIST program for structure searching and to determine if observed fragments are consistent with theoretical fragmentation mechanisms and isotope ratios using MS Interpreter.

Skills Demonstrated:

Videos, handouts, and resources are supplied to aid both teachers and students. Parts 1-4 could be used separately to form a more condensed lab with the most essential parts.

• Searching EI (electron ionization) spectra using the NIST search software
• Processing of EI data files using NIST/AMDIS software
• Drawing chemical structures with drawing programs for transfer to NIST program
• Searching NIST formatted libraries by structure
• Correlating structural fragments in a mass spectrum to substructure using NIST/MS Interpreter
• Creating User Libraries

FREE resources include the following:

• Instructional videos and associated handouts
• Copy of NIST17 Library Search Software
• EI GC-MS data files supplied by NIST for processing with AMDIS
• Additional EI GC-MS files
• AMDIS deconvolution software for processing GCMS data files
• NIST MS Interpreter for understanding and correlating EI fragment ions to substructures
• NIST library of 2,373 EI mass spectra
• Additional EI reference spectra in 5 free libraries (58,456 spectra/34,939 structures)
• ACD ChemSketch structural drawing program for personal and academic use
• Mass Spec Calculator Chemical Drawing Program, free, no limitations

In the fourth part we will look at:

Detailed Handouts including tables of content are available in the LabRulezGCMS library

• Modified Basic Instructions for Using AMDIS with MS Search
• What is AMDIS?
• AMDIS Essentials”
• Opening File with AMDIS
• Deconvoluting Spectra
• Evaluating Deconvoluted Results
• Sending Deconvoluted Spectra to NIST Search Program
• Returning to AMDIS Window after NIST Search
• Uncertain Peaks, Dashed Lines, in Deconvoluted Spectrum
• Avoiding Uncertain Peaks in a Spectrum
• Plotting Single (or Extracted) Ion or (Mass) Chromatograms
• Expanding Chromatograms or Plotting in Log Scale to See Small Peaks
• Manually Processing File in AMDIS
• Adjusting Parameters for Optimized Peak Detection
• Minimizing Marking Components in Chromatogram
• Minimizing Number of Components Detected
• Problem: No Chromatogram/Spectrum Window!

Other parts of this series are focused on:

• Part 1: Very Basic Theory of GCMS Analyses
• Part 2: Installation of Software in Free Laboratory Resource for Universities
• Part 3: EI Mass Spec Library Searches
• Part 5: Understanding EI Fragmentation with MS Interpreter
• Part 6: Structure Searches with Input from ChemSketch
• Part 7: Creating a User Library
• Part 8: Advanced Processing with NIST Software
• Part 9: 58,456 Additional Reference Spectra for NIST Demo Search
• Part 10: AMDIS Difficulties and Ways to Overcome Them
• Part 11: (Advanced) Tracking Complex Coelution with AMDIS and NIST Search