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CHEM 201 Advanced Chemistry Laboratory

Chem 201 Lab 6: GCMS

Lab 6: GCMS of Amino Acids

Equipment:

Varian Saturn 2100T ion trap gas chromatograph-mass spectrometer (GCMS) with a Varian 3900 GC and CP-8400 autosampler

Handouts:

Get from the web: Tutorial on What Is Mass Spectrometry by the American Society for Mass Spectrometry (ASMS)

References:

  • J.B. Lambert, H.F. Shurvell, D.A. Lightner, & R.G. Cooks, Organic Structural Spectroscopy, 1998 (Cook Library: QD272.S6 O74 1998)
    • Part IV: Mass Spectrometry, Chap 14: Fragmentation and ion chemistry
  • R.M. Silverstein & F.X. Webster, Spectrometric Identification of Organic Compounds, 6th Ed., 1998, (Cook Library: QD272.S6 S55 1998)
    • Chapter 2: Mass Spectrometry, pp. 2-70
    • Appendices B & C to Chapter 2 on common fragment ions and common fragments lost (PDF file available)
  • Articles on how quadrupoles and quadrupole ion traps work (PDF files available):
    • MB Denton & PE Miller: The quadrupole mass filter: Basic operating concepts.  J. Chem. Educ. 63: 617-622, 1986.
    • JJ Leary & RL Schmidt: Quadrupole mass spectrometers: An intuitive look at the math.  J. Chem. Educ. 73: 1142-1145, 1996.
    • RE March: An introduction to quadrupole ion trap mass spectrometry. J. Mass Spectrom. 32: 351-369, 1997.
    • KR Jonscher & JR Yates, III: The quadrupole ion trap mass spectrometer--A small solution to a big challenge. Anal. Biochem. 244: 1-15, 1997.
  • Silyl amino acid derivatization and GC articles (PDF files available):
    • CW Gehrke & KR Leimer: Trimethylsilylation of amino acids: Derivatization and chromatography.  J. Chromatogr. 57: 219-237, 1971
    • DL Stalling, CW Gehrke & RW Zumwalt: A new silylation reagent for amino acids bis(trimethylsilyl) trifluoroacetamide (BSTFA). Biochem. Biophys. Res. Commun. 31: 616-622, 1968
    • TP Mawhinney, RSR Robinett, A Atalay & MA Madson: Analysis of amino acids as their tert.-butyldimethylsilyl derivatives by gas-liquid chromatography and mass spectrometry.  J. Chromatogr. 358: 231-242, 1986
    • CJ Biermann, CM Kinoshita, JA Marlett & RD Steele: Analysis of amino acids as tert.-butyldimethylsilyl derivatives by gas chromatography.  J. Chromatogr. 357: 330-334, 1986
    • HJ Chaves Das Neves & AMP Vasconcelos: Capillary gas chromatography of amino acids, including asparagine and glutamine: Sensitive gas chromatographic-mass spectrometric and selected ion monitoring gas chromatographic-mass spectrometric detection of the N,O(S)-tert.-butyldimethylsilyl derivatives.  J.Chromatogr. 392: 249-258, 1987
    • RJ Early, JR Thompson, GW Sedgwick, JM Kelly & RJ Christopherson: Capillary gas chromatographic analysis of amino acids in blood and protein hydrolysates as tert.-butyldimethylsilyl derivatives.  J. Chromatogr. 416: 15-23, 1987.
    • C-J Goh, KG Craven, JR Lepock & EB Dumbroff: Analysis of all protein amino acids as their tert.-butyldimethylsilyl derivatives by gas-liquid chromatography.  Anal. Biochem. 163: 175-181, 1987

Lab description:

Get a PDF of

  • the lab experiment
  • a full-page chart showing individual amino acids and their functional group structures (see abbreviated version below)
  • tables listing amino acids, their chemical composition, their major fragments and their exact weights for TBDMS by EI.
  • tables listing the theoretical abundances of the [M+1] , [M+2], [M+3], ... ions relative to the M ion for common amino acid derivatives and GCMS ionization modes shown above.
Where:
TBDMS = t-butyldimethylsilyl
EI = electron impact ionization

amino acid structures

Last modified February 15 2012 11:38 AM

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