Refurbished Hewlett Packard (Agilent) 5988A GC/MS System

The HP 5988A GC/MS system is a versatile research-grade mass spectrometer (MS) interfaced with a 5890A gas chromatograph (GC), and has the capabilities of separating volatile mixtures, as well as mass analysis of low molecular weight, volatile, nonionic, thermally stable components. Following separation by gas chromatography, the mass spectrometer separates and identifies (i.e., via an extensive library search option) ionized atoms or molecules based on their mass-to-charge ratios (m/z). One can obtain structural information about the compound from fragmentation patterns that arise from electron impact ionization. This instrument can also employ multichannel detection and quantitative analysis.

Sample preparation involves the dilution of the analyte in an organic solvent, such as hexane, methanol, or ether, which does not contain water or halogen-containing compounds. About a micro liter of the sample is injected into the heated inlet of the GC column via a syringe in either an on-column or a split/splitless mode. The column that is currently installed is a fused-silica capillary column, which can be easily replaced without venting the source and the analyzer manifolds and without using isolation valves. The mass spectrometer houses an ion source that has both electron impact (EI) and chemical ionization (CI) capabilities, but it is typically operated in EI mode to produce only positive spectra of the ionized vapor. The dual source is temperature controlled to assure vaporization of the components eluting from the GC column. This system also has the potential to accommodate fast atom bombardment, desorption CI, and thermospray ionization, but it is not currently used in these modes.

The mass analyzer is a hyperbolic quadrupole mass filter containing four 203 mm long rods and an entrance lens that minimizes rod contamination. The analyzer is capable of scanning an entire spectrum in a mass range of 10 to 1000 amu, and it is particularly well suited for selected ion monitoring. It also contains a high mass option that extends the normal mass range to 2000 amu. The ion signal is detected using an electron multiplier assembly that effectively amplifies the ion signal. The mass spectrometer maintains a high vacuum system that houses the operating elements of the MS. The ion source, entrance lens, mass filter, and detector are all under high vacuum conditions. Normal vacuum levels in the MS are about 1*10-6 torr for electron impact ionization, and 1*10-6 to 6*10-4 torr for chemical ionization. When in chemical ionization mode, the system is differentially pumped in order to reach appropriate vacuum for entering the mass analyzer. For this system, a differential pumping system using two reliable diffusion pumps is used to provide fast pumping for both the ion source and the analyzer chamber. A turbomolecular pump can also be used in place of the diffusion pump. This system will automatically shut down if the pressure becomes too high. In order to guard against surface contamination, the mass analysis system is made of stainless steel.

Specifications of the HP 5988A GC/MS system include a mass stability of +/- 0.13 amu for an eight-hour period and a mass accuracy of +/- 0.13 amu within the calibrated mass range. The sensitivity of this instrument, for electron impact ionization, is when a nanogram of methyl stearate is scanned from 290 to 310; it should produce a signal-to-noise ratio of 10:1 at the molecular ion, m/z 298.3. The ionization energy can be adjusted from 10 to 280 eV. The MS has a scan speed with a maximum rate of 2000 amu/sec. The ion source temperature is digitally controlled in +/- 2 °C steps from ambient 100 to 300 °C, and the dynamic range is about 2*106. This GC/MS system is typically used to analyze relatively small organic molecules and their mixtures. The majority of users are organic chemists attempting to identify an unknown product or to assure that the correct product has been synthesized. Barney Ellison’s group simply uses this instrument to verify that their pre-radical structure is azoethane and not some unwanted side-product. Veronica Viada’s group processes organic monolayers with OH radicals and/or O3. They use the GC/MS to see if any products may have formed, as well as to separate and identify their products. For example, hexadecane is processed with OH radicals, and ketones were seen in the chromatogram. From the mass spectrum, they can actually see where on the organic monolayers the ketones resided. The following is an example spectrum provided by the Viada group. Notice that one can obtain both a chromatogram and a mass spectrum for each peak on the chromatogram, and subsequently identify each peak from the chromatogram by comparing to a library database of electron impact ionization mass spectra. Other applications of the GC/MS system include such analyses as wastewater contamination, pesticide analysis, organic purity, and even isotope exchange reactions.