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====== Gas Chromatograph/Mass Spectrometer ======
  * Manufacturer - Hewlett Packard
  * Model Number - HP 5890 II 
       * Shown with Autosampler (on right)

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======Theory======
     * Six Basic Principles in Performing Gas Chromatography:
          * Flow Controller
          * Sample Introduction Device
          * Column
          * Oven
          * Detectors
          * Computer Interface (Data Management)

====Gas Chromatography====
          * Process involves the physical separation of compounds in a mixture by injecting the mixture into a tube (column) that contains a silica based inert compound.  The mixture is called the mobile phase and the silica compound is known as the stationary phase.  A carrier gas is used to flush the mobile phase through the column.  The stationary phase will pass some compounds and slow down others.  
          * Compounds in mixture are identified by their retention times.
               * Retention time is the time it takes for the individual compound to pass through the entire column.

====Mass Spectrometry====
          * Mass spectrometry deals with shattering compounds into component ions by passing sample through an ionization (high voltage) source. 
          * The ions are separated by a large magnetic or electric field.  The ions are then collected in "traps" and then analyzed.  A charge to mass ratio is calculated and a mass spectra is generated.  

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======Interface and Equipment======

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====GC Column====
          * Capillary tube of length between 1 to 100 m and thickness range of 0.25 to 5 mm
          * Column is either packed with silicone based stationary phase or inside is coated with the material.

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====Hardware====

     * Nitrogen Gas Cylinder  
          * Carrier gas for mobile phase, non-reactive and inert to sample being tested
     * Hydrogen Gas Cylinder  
          * Used to combust sample at the end of the analysis
     * Plumb Lines 
          * To connect cylinders to GC/MS
     * Vacuum Pump  
          * Used for MS which operates under low pressure conditions
====Computer Interface====
     * The GC/MS can either be run automatically or manually.
          * Both require use of computer program.
               * PC and software are Windows based.
               * Software contains program that controls oven temperature such that the oven starts at a low temperature and ramps up to a higher temperature at different heating rates.               
       
======Calibration======
     * Calibration standard is made of a pure compound (e.g. bromofluorobenzene) and is used for quality control of the GC/MS.  
     * The compound has a specific retention time and a specific mass spectra.  
     * Quality control is usually done at after a fixed number, usually 20, of samples have been analyzed.
     * Quality assurance is done whenever the instrument cannot be calibrated.
          * QA steps include:
               * Changing the check standard - an aged check standard can affect accuracy of instrument
               * Conditioning the column - bake the column to a temperature of 300<sup>o</sup>C to remove contaminants
               * Replacing the column - cracks and fissures
               * Checking the carrier gas flow rate - mobile phase may be going faster or slower than normal
               * Replacing the entire instrument - GC oven may be irreparable, internal plumbing damaged, etc

======Purpose and Performance======
     * A combined GC/MS has the ability to detect minute quantities of a solute contained within a larger volume of solvent.  For example, a properly calibrated GC/MS can quantify organic contaminants, such as volatile organic carbons (VOC) on the order of parts per billion present within large volumes of soil, water or air.  
          * This is useful in environmental sampling especially when looking for compounds that adversely affect human health.
          * Liquid or air samples on the order of milliliters can be sampled.
               * If using the direct inject method, microliters of sample are usually used.
     * Sample Injection
          * Non-Direct Inject
               * Usually done with help of autosampler.
               * Nitrogen gas is bubbled into a tube containing sample to draw out the volatile parts of the mixture.
                    * Semi or non-volatile compounds are not usually sampled by GC.
               * Mixture is held in a trap until GC signals the computer to start the oven program.
               * Mixture is injected into the inlet of both the GC and MS at the same time.  Both instruments collect data at the same time.
               * As the compound is sent through and out of the column, the MS shatters each compound into ions as they are ejected and quantifies their mass spectra.
               * At the end of the column, there is a flame ionizing detector, FID, which combusts the sample with the aid of hydrogen gas.
                    * The GC quantifies the amount of burn and the time of ionization to render a retention time and concentration.
          * Direct Inject
               * Analyst will start computer program and inject sample at same time rather than using autosampler.

======Data=====          

{{:atmos:535:projects:scan2.jpg|}}

     * Top picture shows the chromatogram.
          * Chromatogram shows peaks for each compound in the mixture according to retention time.  It also shows concentrations of the compounds.
          * Integrated area of peak is the concentration.
     * Bottom picture shows the mass spectra.
          * Using the reference spectra library that comes with the GC/MS software, an analyst can identify each peak by clicking on the highest point of the peak.
          * At the end of the mass spectra is the molecular weight of the ion.
               * For example, chloroform is a chlorinated VOC with molecular weight of 119.5 g/mol.  The ion molecular weight will be somewhere between 116 and 118 g/mol.  The discrepancy is due to isotopes of carbon and chlorine.

======Usage and Deployment======   
     * Liquid samples are collected in bottles and air samples are collected in bags.
          * Air samples can be direct injected into GC/MS from the bag instead of by autosampler or syringe as with liquid samples.
          * Does not perform real time sampling.
          * In a production laboratory setting, a GC/MS can be dedicated to performing emergency sampling which requires a fast turn around.
          * Most samples that are being tested for VOCs have an average sampling time of 30 minutes from injection to the end of the analysis.      
     * GC/MS is designed to be used in a stationary environment.
          * Complex setup of GC, MS, computer interface, carrier gas cylinders, and plumbing make it difficult to use in a mobile setting (e.g. aircraft).
          * Less sophisticated instruments can be used in mobile platforms.
               * Martian land rover has onboard GC/MS but uses much less sophisticated sampling techniques due to space constraints.
     * Fields Other Than Environmental and Space Science GC/MS Is Used for
          * Forensic Science
          * Toxicology
          * Drug Screening
          * Pesticides
     * Power Consumption
          * GC/MS can be used on standard 120 V (220 V if 50 Hz cycling alternating current) power line but requires high current for MS.
          * 800 W power consumption
     * Cost
          * $40,000 for GC/MS combination
          * $1000 for PC and software
          * $500 for gas cylinder - lasts approximately three weeks with 24 hour consumption

======Acknowledgments and References=====

     * GMI, Inc - [[http://www.gmi-inc.com/Products/HP%205890%20GC.htm]]
     * University of North Dakota, Chemistry Department, Abbott Hall GC/MS Lab
     * HP 5890 GC/Agilent 5973 MS User Manual 
     * TestAmerica Labs, Inc (Formerly Severn Trent Labs), Edison, New Jersey