Instruction/Users Manual
 Hewlett-Packard Gas Chromatograph-Mass Spectrometer
 St. Olaf College Chemistry Department

 I. Instrument Overview

The department GC-MS is housed in the organic synthesis lab (SC 311) and is composed of the following components: Hewlett-Packard 5890A Gas Chromatograph; Hewlett-Packard 5790B Mass Selective Detector; Hewlett-Packard 59822A Gauge Controller; and a Hewlett-Packard Vectra Series 3 PC running MS ChemStation G1034C software.

Guidelines for GC-MS Use

  1. ALL samples must be filtered prior to injection.
  2. No unapproved organometallic species injected...pass solution through bed of silica gel to remove various metals and other impurities prior to analysis.
  3. Always thoroughly wash the syringe after injections with acetone, dichloromethane, or other suitable solvent.
  4. Avoid use of low volatility solvents; if unsure, try using ethyl acetate or isopropanol.
  5. Use the Solvent Flush Injection method (see below) to inject approximately 1 mL of sample.
  6. The maximum ion signal one should aim to generate is 1.00E+06 (1.0E-02 M for split injection - comparable to NMR analysis - and 1.0E-04 M for splitless) for 1-mL injections.
  7. Use a sufficiently long solvent delay on the MSD; avoid detecting solvent peaks to increase MSD filament lifetime.
  8. Active compounds (amines and alcohols) may need derivatization prior to GC-MS analysis. Make either a trimethylsilyl, acetyl, or trifluoroacetyl derivative.

Gas Chromatograph (S/N 2541A06271)

The gas chromatograph is equipped with dual capillary column injection ports, a flame ionization detector (FID), and an internal column switching valve attached to the FID and MSD. Helium is delivered to the GC with a pressure of 56 PSIG and the tank should be changed when the total tank pressure falls to 200 PSIG. Back-pressure on the head of the column should be set at ~15 PSIG for both injection ports. The MS ChemStation software controls the GC temperature settings; however, the user can override the computer by entering values on the instrument keypad. The GC oven temperature should not exceed 300 °C as higher operating temperatures will result in column degradation.

Mass Selective Detector (S/N 2513A01010)

All variables are controlled through the MS ChemStation Software. The user should check the following conditions prior to use: remove the MSD from Standby and enable interface Heating by pressing the appropriate buttons on the front panel of the unit. Lights behind the buttons indicate that the particular feature is active. Heating desorbs gases from the MS interface and releasing Standby establishes an appropriate vacuum range via bringing the turbopump to maximum speed. Check the pressure in the MSD prior to use; turn on the power to the gauge controller and filament. The gauge reads ~5.0E-05 torr when the oven temperature is 100 °C; the selector switch indicates the power of 10. Turn off the filament and gauge controller prior to an analysis.



Upon finishing with the instrument for the day, return the MSD to standby, decrease the TOTAL FLOW on the Injector Ports until the meter reads ~4. If you are finished for the weekend or extended time period, reduce the injector and oven temperatures to 50 °C by using the GC keypad.

MS ChemStation Software

The GC and MSD are controlled by a PC running MS ChemStation software. This package permits instrument control, data collection, and data processing. The specific control and processing software commands needed for a specific injection is intimately related to the injection technique. For general use or analysis in the organic laboratory, see the section under Split Injections. For trace analytical work you will want to use Splitless Injection.


Solvent Flush Injection

  1. Repeatedly fill and flush the syringe with solvent to wet the needle and barrel.
  2. Immerse the needle in the desired solvent and retract the plunger until you reach a value of 1.2 mL (needle volume is ~0.8 mL for a Hamilton 701 syringe, giving you a 2-mL flush).
  3. Remove the syringe from the solvent and retract the plunger until an air pocket is observed on the syringe end of the needle.
  4. Place the syringe into the sample solution and draw the desired amount into the syringe by moving the plunger the exact amount.
  5. Remove the syringe from the solution and draw the plunger back until the sample is in the barrel between two air pockets.
  6. The exact sample size can be read off the barrel and the sample is ready for injection.
Since solvent is behind the sample, this ensures that the entire sample is flushed into the injector without "hang up".. When the septum of the injector port is penetrated, the injection should be made rapidly. With practice this technique yields injection-to-injection reproducibilities as good as ±1% peak height variation. Be sure to thoroughly clean the syringe after injection to avoid carryover.