GasChromatography/ Mass Spectrometry GC/MS

Identificationof unknown compounds using Gas Chromatography Mass Spectrometry GC/MSmethod


Themain aim of this experiment was to identify the unknown compounds 1,2 and 3 using gas chromatography-mass spectrometry (GC/MS). Thespectra and peaks of the unknown compounds were compared with thoseof the six standard samples of straight alkane, aromatic halide,alkyl halide, aromatic ether, aromatic halide, and alkane. Theunknown compounds were identified as those of alkane, alkyl halide,and aromatic halide respectively. The identification was based on thepeak results that were closer to the three standards. The experimentwas conducted by running the unknown compound and the standardsthrough GC/MS using chemstation software. It can, therefore, beconcluded that all the objectives of the experiment were achieved.The method was noted as faster and easy to conduct compared to theothers available. It was also observed to be a more accurate waysince it quantitatively provided the mass of individual components ofa compound.

Themain aim of this experiment is to analyze the unknown mixtures ofsubstances using a high-resolution gas chromatography combined withion trap detector which (ITD) is a variation of the quadruple massspectrometer. The experiment will rely on the ability of ITD tooperate as a gas chromatography detector. The IDT mass spectrum of asubstance will be compared to the classical impact electron massspectrum of a standard derived from the national bureau of standardslibrary. The comparison is also made with reference to EI ofdifferent organic compounds. This will enable identification ofcharacteristic features of the mass spectrum of a class of substanceshence determination the chemical structure of the compound. Theexperiment will also involve the use of NIST 2005 library softwarethat supports GS/MS data acquisition system to confirm theidentification of the unknown components of the unknown substances(Lab Manual).

Gaschromatography has been defined as a method of separation of mixturesthat depends on the adsorption and solubility of the separatingcompounds. GC method of separation is considered physical since thecomponents are distributed between two phases. These include thestationary and the mobile phase. The mobile phase is normally the gasthat moves through the stationary segment composed of solidcomponents. The method is also known as gas-solid chromatography.This method has been applied in the separation of gasses in gaseoussolution and analysis of residual gasses in high volume systems(Georgia State University).

Massspectrometry, on the other hand, is a measure of the mass andrelative atomic mass (RAM) of atoms and molecules. The method isnormally done by the use of a spectrometer, which applies themagnetic force on accelerating charged particles. The principlebehind the method is that atoms of a molecule are excited throughionization followed by acceleration and movement of the ions into amass spectrum region. The radius of path electron and mass aredetected using ion electron detector thereby determining the mass ofa molecule. Since magnetic force is always perpendicular to thevelocity, a centripetal force is generated equal to the radius of thepath produced by the magnetic field. A velocity selector only choosescharged particles in the mass spectrometer through the mechanism ofopposing electric and magnetic force. The sensitive isotope detectorspresent in mass spectrometer quantifies substances based on theirmasses. A combination of mass spectrometry and gas chromatography hasalways been used for the identification of trace elements in toxinsand other substances. The method has also been applied in satellitesand spacecraft for the identification of small particles present inspace (Lab5).This experiment will employ the Gas-liquid chromatography with aporous solid stationary phase covered with absorbing liquid and amobile gaseous phase. The other objectives of this experiment willinclude identifying the unknown substances using GC/MS method.


Sixstandards were provided for this experiment. These included thestraight alkane, aromatic halide, alkyl halide, aromatic ether,aromatic halide, and alkane respectively. Also provided were threeunknown substances that were composed of a mixture of two or more ofthe six standards provided. The substances and the unknown compoundswere run through GC/MC and their retention time and spectra peaksrecorded using chemstation software known as GC/MSD 6890N software.The results of the unknown substances were compared with those of thestandards to identify the unknown compounds. The MSDCHEM method ofthe software was used to run the unknowns using the samples placed intheir respective vials. Peaks of the substances were observedappearing on smaller windows of the program and analysis of thefilaments conducted.


Figure1: Mass spectrum of standard 1 Run 3 for straight alkane

Figure2: Mass spectrum of standard 2 Run 2 for aromatic halide

Figure3: Mass spectrum of standard 3 Run 1 for alkyl halide

Figure4: Mass spectrum of standard 3 Run 1 for alkyl halide

Figure5: Mass spectrum of standard 4 Run 1 for aromatic ether

Figure6: Mass spectrum of standard 5 Run 1 for aromatic halide

Figure7: Mass spectrum of standard 6 Run 1 for alkane

Figure8: Mass spectrum of unknown 1 Run 1 compound

Figure9: Mass spectrum of Unknown 1 Run 1 compound

Figure10: Mass spectrum of Unknown 2 Run 1 compound

Figure11: Mass spectrum of Unknown 2 Run 1 compound

Figure12: Mass spectrum of Unknown 3 Run 1 compound

Figure13: Mass spectrum of Unknown 3 Run 1 compound

Figure14: Peak comparison for the six standard samples and unknown 1compound under different runs

Figure15: Peak comparison for unknown compound2 and 3 for different runs

Figure16: Mass spectrum of PARABEN 4 Run 1 compound

Figure17: Mass spectrum of PARABEN 1 Run 1 compound


Theresults indicated that standards 1 to 6 had different peaks when runthrough GC/MS software. The standard 5 aromatic halides had a highpeak height of 1047685 with standard 1 having the highest peak heightof 1089980. Unknown compound 1 had a peak height of 1096365 that wasalmost similar to that of standard 1 hence identified as the straightalkane (Figure 14). Unknown compound 2 had a peak height of 1685514indicating that it had substances from the straight alkane and alkylhalide. Unknown compound 3, on the other hand, had a peak height of363293 showing that it had elements from standard 4 and standard 6,which were aromatic ether and alkane (Figure 15). The spectra of theunknown compound 1 (Figure 8 &amp 9) was almost similar to standard3 confirming that it consisted of alkyl halide substances (Figure 1).The unknown compound 2 spectrum (Figure 10) was similar to that ofstandard 2 (Figure 2). This indicated that the unknown compound 2contained components of aromatic halide. The unknown compound 3(Figure 11), on the other hand, had a spectrum similar to standard 5(Figure 5) thus indicating that it contained aromatic halidecomponents.

Theseresults were inconsistent with others obtained using this softwarefor previous studies. The experiment had been conducted usingchemstation software. The software has advantages over the othermethods in that it helps in the separation of the actual componentsof unknown substances quantitatively, and in the determination of thestructure using ITD technique. The elements of the unknown substanceswere identified based on the retention time and mass spectrumcomparisons with standards (Figure 11, 12 $ 13).

TheGC/MS involved the use of 30cm capillary column composed of packedcolumns. The components of separated mixture moved to ion trapdetector as pure compounds and were ionized when they passed throughthe stream of gas over a beam of electrons accelerated at 70eVthereby inducing an electron impact on the substances. As a result,the bonds of the compounds were separated inducing different internalenergy. Fragmentation as a result of ion excitation occurredresulting in the formation of the molecular ion. Given that theatomic mass of a molecular ion is similar to that of a neutralmolecule, it was simpler to determine the mass of the unknownsubstance. The software detected the neutral ions and resulted in theproduction of mass spectra.

Theresults were compared to the mass spectra from the standard librarycontaining different spectra for various elements and compounds. Thepeaks of the unknown compounds were, however, not above 150 asindicated in the spectra suggesting that they had a mixture ofdifferent substances. The possible source of error that may haveprevented the determination of accurate results included the use ofstandards that had been run instead of using the library data thathad some variations (Skoog,Holler, and Stanley, n.p).

Theother possible sources of error included the retention timemeasurement for each substance, which may have varied depending onthe timer thus, resulting in different peaks. A possible improvementcan be adapted following the application of standard data from thenational libraries run using other advanced software.


Itcan, therefore, be concluded that the unknown compounds wereidentified successfully as consisting of elements from the straightalkane, alkyl halide, and aromatic halide respectively. GC/MC wasalso proved as an accurate and reliable quantification method for thedetermination of components of substances. The objectives of theexperiment were also realized given that the unknown compounds wereidentified successfully.


GeorgiaState University. MassSpectrometer.Hyper Physics, n.d. web. 10 July 2016.

&quotLab5: Gas Chromatography/Mass Spectrometry (GC/MS).&quot – Chemwiki.N.p., 02 Oct. 2013. Web. 27 June 2016.Skoog,Douglas A., F. James Holler, and Stanley R. Crouch. Principlesof Instrumental Analysis.N.p.: n.p., n.d. Print.