Gas chromatography-mass spectroscopy (GC-MS)

Gas chromatography-mass spectroscopy (GC-MS) is actually two techniques that are combined to form a single method of analyzing mixtures of chemicals. The IC-FAS housed Agilent’s 7890A GC that takes our lab to the next level of GC and GC/MS performance, including advanced separation capabilities. Faster oven cool-down and robust back flushing let us get more samples done in less time. Our instrument is coupled to the Agilent 5975C inert MS with Triple-Axis Detector that gives advanced analytical capabilities that enhance our results and our confidence. In addition to delivering better MS resolution and the lowest mass deviation available, the system offers superior sensitivity and spectral integrity. Advanced analysis routines let us get more information from every run, and the latest version of automated spectral deconvolution, identification, and quantification software provides higher quality analyses with even less operator time and attention.

Sample Preparation Guide

Sample preparation is a very critical step in chromatographic analysis and often takes significant portion in total analysis time. The main objectives of sample preparation are,

(a) to minimize interferences

(b) to prepare sample as to compatible with instrument. This ensures no damage to the column or instrument

(c) to comply with standard methods of analysis

Proper sample preparation will ensure accurate and reproducible results. The following Figures indicate time spent on typical chromatographic analysis and possible sources of errors occur during analysis.

Method of sample preparation for the GCMS is highly dependent on the compounds that are analyzed. Therefore, it is recommended to conduct a literature review of similar samples or standard methods available when preparing samples. Instrument center do not have any facility to prepare samples.

Specifications and Settings of the GCMS instrument

GC instrument Agilent 7890A
MS instrument Agilent 5975C inert XL EI/CI MSD with triple axis detector
Auto sampler Agilent 7693

(HP 5 ms ultra inert)


  • Excellent for trace level analysis of acids and bases, such as semivolatiles analysis
  • (5%-Phenyl)-methylpolysiloxane, identical selectivity to HP-5MS
  • Specifically tested for inertness for active compounds including acidic and basic compounds
  • Improved signal-to-noise ratio for better sensitivity and mass spectral integrity
  • Non-polar with very low bleed characteristics, ideal for GC/MS
  • Bonded, cross-linked and solvent rinsable
  • Equivalent to USP Phase G27
  • Similar Phases: Rtx-5ms, Rxi-5ms, Rxi-5Sil MS, PTE-5, BPX-5, AT-5ms, ZB-5ms, SLB-5ms, Equity-7
Carrier gas He
General classes of compounds analyzed Trace level analysis, alkaloids, drugs, FAMEs, halogenated compounds, poly aromatic compounds, Fatty acids (derivertized as methyl esters), pesticides, plant extracts, essential oils, solvent purity check
Common solvent matrices used Hexane, chloroform, acetone, ethyl acetate, methanol, absolute ethanol (please ensure solvent has HPLC grade purity)

* for any other specification please contact instrumental assistant

General instruction when using GCMS

  • GCMS is a technique that very sensitive to moisture. Therefore, use of HPLC grade or double distilled and dry solvents are recommended. No aqueous samples. Always use dry glassware when preparing samples. These will ensure long life of the column and instrument. Check reference 1 for more details.
  • Compounds that are analyzed using GCMS should be volatile. Check method to remove any non-volatile compounds, ionic compounds. If a non-volatile compound need to be analyzed, make sure to use appropriate derivertizing agent or pyrolysis method prior analysis.
  • Sample should be transparent and free of any precipitates, emulsions, cloudiness
  • GCMS column that is currently in use is a non-polar column. Please refer column details in reference 2 to check compatibility.

What you need to bring when analyzing GCMS samples

  • Reserve your time ahead and submit GCMS request form (signed by the supervisor and the instrument coordinator)
  • Sample (transparent, not highly concentrated, moisture free, labeled (“sample no._student name_dept name/supervisor initials”)
  • Literature related to analysis (to set GCMS parameters (eg. He flow rate, split/split less, temperature profile, etc. for the compounds that are analyzed)
  • Blank (usually the solvent matrix without the analyte)
  • Payment slip (please refer payment section)
  • Empty CD to transfer data

Further reading




Dr. Dakshika Wanniarachchi

Click following link for the reservation of the GCMS instrument