GAS CHROMATOGRAPHY - MASS SPECTROMETRY

A BASIC INTRODUCTION

by

Frank M. Dunnivant and Jake Ginsbach

Whitman College

Chemistry Department

Walla Walla, WA  99362

Acknowledgements/Funding

Funding for the purchase of our Agilent GC-MS came from the M. J. Murdock Charitable Trust, Whitman Alumni, and Whitman College.  The preparation of this Ebook was funded by the Louis B. Perry Summer Research Scholarship grant program at Whitman College.

Reviewers: 

-Noah Bronstein, Undergraduate chemistry student at Whitman College

-Laura Sanchez, Ph.D. student in the chemistry program at UC Santa Cruz

-Grady Blacken, Ph.D. student in the chemistry program at the University of Washington

-Noah Bronstein, Undergraduate chemistry student at Whitman College

-Marion Gotz, Assistant Professor at Whitman College

-Laura Sanchez, Ph.D. student in the chemistry program at UC Santa Cruz

-Tommaso Vannelli, Assistant Professor at Gonzaga University

-Skip Wade, Professor Emeritus at Whitman College

Intended Reader:  Undergraduate students who has taken organic chemistry, analytical chemistry, and instrumental methods of analysis.  Also, beginning graduate students, who are not well versed with instrumentation, will also find this book helpful.

CHAPTER 1

The Basics of Gas Chromatography and Mass Spectrometry

1.1 Introduction

1.2 Types of Samples and Samples Introduction

1.3 Chromatographic Theory

1.4 The GC of GC-MS

1.5 The MS of GC-MS

1.5.1 Analyte ionization

1.5.1.1 Ionization Techniques for Solid Non-Volatile Analytes:

1.5.1.1a Field Desorption

1.5.1.1b Matrix Assisted Laser Desorption/Ionization, MALDI

1.5.1.2 Ionization Techniques for Volatile Analytes Entering the MS from a GC

1.5.1.2a Electron Ionization or Electron Impact (EI)

1.5.1.2b Chemical Ionization (CI)

1.5.2 Repulsion and Accelerator Plates, Slits, and Electronic Focusing Lens

1.5.3 Common Mass Filters (Mass Analyzers)

1.5.3.1 Magnetic sector mass filter

1.5.3.2 Quadrupole mass filter

1.5.2.3 Quadrupole ion trap mass filter

1.5.3.4 Time-of-Flight (TOF) mass filter

1.5.3.5 Double Focusing Systems

1.5.3.6 Tandem Mass Spectroscopy

1.5.4 Detectors

1.5.5 Three-Dimensional Aspects of GC-MS

1.6 Summary

CHAPTER 2

Fragmentation and Interpretation of Spectra

2.1 Introduction

2.2 Creation of the Spectra

2.3 Identifying the Molecular Ion Peak

2.4 Use of the Molecular Ion

2.5 Identification of Analytes using Isotopic Ratios

2.6 Fragmentation

2.7 Rearrangements

2.8 Identification of Compounds

2.9 Fragmentation of Hydrocarbons

2.9.1 Fragmentation of Straight Chain Alkanes

2.9.2 Fragmentation of Branched Alkanes

2.9.3 Fragmentation of Cyclic Alkanes

2.9.4 Fragmentation of Alkenes

2.9.5 Fragmentation of Aromatics

2.10 Fragmentation of Alcohols

2.11 Fragmentation of Ketones and Aldehydes

2.11.1 Ketones

2.11.2 Fragmentation of Cyclic Ketones

2.11.3 Fragmentation of Aromatic Ketones

2.11.4 Fragmentation of Aldehydes

2.12 Fragmentation of Carboxylic Acids

2.13 Fragmentation of Ethers

2.14 Fragmentation of Esters

2.15 Fragmentation of Amines

2.16 Fractionation of Amides

2.17 Fragmentation of Nitriles

2.18 Reviewing General Principals

2.19 Searchable Databases

CHAPTER 3

Really Cool Pedagogical Experiments with Interpretation of Results

3.1 Preliminaries

3.1.1 Instrument and Instrumental Settings

3.1.2 Trouble Shooting

3.1.3 Maintenance

3.2 Illustrative Experiments of Fundamental Concepts

3.2.1 Advantages of GC versus MS

i.  The lack of separation of 2,2’-DCB versus 2,6-DCB in capillary column GC, but confirmatory identification using MS

ii.  The separation of cis versus trans compounds by GC but lack of confirmatory identification by MS

3.2.2 The Dependence of Ionization Source on Fragmentation, Molecular Ion, and Structure

i.  Hard versus soft ionization sources

ii.  Positive versus negative chemical ionization sources

3.2.3 Synthesis experiments and spectra interpretation

3.3 Analytical Experiments with an External Reference Standard

3.3.1 Caffeine Concentrations in Human Urine

3.3.2 Nicotine Concentrations in Human Hair

3.3.3 Drug screen of Urine

3.3.4 Bisphenol A Concentrations in bottled Everclear

3.3.5 Cocaine Residues on Dollar Bills

3.4 Analytical Experiments without an External Reference Standard

3.4.1 Identification of Components in Whiskey

3.4.2 Identification of Fragrances