University of Vermont

CHEM 201: Advanced Chemistry Laboratory

Chem 201 Lab 6: GCMS

Lab 6: GCMS of Amino Acids


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

Handouts & References:

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

  • 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)
  • Silyl amino acid derivatization and GC articles:
    • 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.
TBDMS = t-butyldimethylsilyl
EI = electron impact ionization

amino acid structures

Last modified January 06 2016 04:02 PM