Mass Spectrometer

High resolution mass spectra provide information on chemical composition. The department operates a
an Extrel Benchmark GC/Thermabeam/LC/MS. The hyphenated techniques of gas chromatography-MS and liquid chromatography-MS permit the composition of complex mixtures to be analyzed. A range of other sample introduction and ionization systems are available. Instruments are equipped with dedicated data systems for acquisition and data manipulation. The spectrometer is located in building 65 room 230 and is currently configured for LC/MS; however, the LC aspect is only a high pressure pump to deliver a methanol solution of the unknown pure compound, not mixtures. There are several web sites which provide tools such as calculating the exact mass of a molecule (a link to SIS)..

Select Properties from the Toolbox window, then select Instrument and Thermobeam from the menu. Push the Reset button on the leftmost board in the BME cage of the MS than select Apply and Start. A series of messages will flash through the bottom of the Toolbox window, showing the progress of file loading. Wait for the red light on the CPU board to indicate the system is ready to operate. The complete procedure is also attached to the instrument login book.

Shut-Down Procedure -- Disconnect the interface. Lower the nebulizer control temperature. Wait a few minutes and shut down the flow of helium. Lower Expansion region temperature and shut down the desolvation pumps. Check the nebulizer tip temperature and stop solvent flow through the capillary. Turn off the solvent pump. Check the mass spectrometer status again. Turn off the monitor screen.

What are mass spectrometers used for? Mass spectrometers are used for all kinds of chemical analyses,ranging from environmental analysis (e.g. detection of poisons such as dioxin) to the analysis of petroleum products, trace metals and biological materials (including the products of genetic engineering).

What does the mass tell us? Let us use water (H₂O) as an example. A water molecule consists of two hydrogen (H) and one oxygen (O). The total mass of a water molecule is the sum of the mass of two hydrogen (approximately 1 atomic mass unit per hydrogen) and one oxygen (approximately 16 atomic mass units per oxygen):

Introduction -- Mass spectrometers use the difference in mass-to-charge ratio (m/e) of ionized atoms or molecules to separate them from each other. Mass spectrometry is therefore useful for quantitation of atoms or molecules and also for determining chemical and structural information about molecules. Molecules have distinctive fragmentation patterns that provide structural information to identify structural
components.

The ion separation power of a mass spectrometer is described by the resolution, which is defined as:
R = m / m, where m is the ion mass and m is the difference in mass between two resolvable peaks in a mass spectrum. e.g., a mass spectrometer with a resolution of 1000 can resolve an ion with a m/e of
100.0 from an ion with an m/e of 100.1.

Instrumentation -- In general a mass spectrometer consists of an ion source, a mass-selective analyzer, and an ion detector. Since mass spectrometers create and manipulate gas-phase ions, they operate in a high-vacuum system. The magnetic-sector, quadrupole, and time-of-flight designs also require extraction and acceleration ion optics to transfer ions from the source region into the mass analyzer. The details of mass analyzer designs are discussed in the individual documents listed below. Basic descriptions of sample introduction/ionization and ion detection are discussed in separate documents on ionization methods and ion detectors, respectively.

Vacuum Pumps -- The two important parameters of a vacuum pump are its lowest attainable pressure, and its pumping speed, typically listed as liters per minute (lpm) or cubic feet per minute (cfm). The lowest attainable pressure depends on the design of the pump as listed in the following table. The pumping speed of the different types of pumps depends on the physical size of the pump.

Types of Vacuum Pumps

Pump	Lowest Pressure, Torr	Typical Use
Mechanical pump	10-1 to 10-3	roughing /backing pump
Diffusion pump	10-6	vacuum lines
Turbomolecular pump	10-9	high-vacuum systems

Mechanical pumps consist of an inlet, and exhaust with a one-way valve, and an off-center rotating
piston in a cylindrical cavity. As the piston rotates, gas is pulled into the cavity, and forced out
through the exhaust port. The rotating piston has spring-loaded vanes to create a seal with the cavity
walls. This seal, and the exhaust port valve, are lubricated with a low-vapor-pressure oil. A
two-stage mechanical pump consists of two pumping cavities in series to achieve a lower vacuum
pressure. Accessories needed when using mechanical pumps are a mist filter (or vent) to trap oil mist
in the pump exhaust, and a trap to prevent oil vapor from back streaming into the volume being
evacuated.

Quadrupole -- A quadrupole mass filter consists of four parallel metal rods arranged as in the figure below. Two opposite rods have an applied potential of (U+Vcos(wt)) and the other two rods have a potential of -(U+Vcos(wt)), where U is a dc voltage and Vcos(wt) is an ac voltage. The applied voltages affect the trajectory of ions traveling down the flight path centered between the four rods. For given dc and ac voltages, only ions of a certain mass-to-charge ratio pass through the quadrupole filter and all other ions are thrown out of their original path. A mass spectrum is obtained by monitoring the ions passing through the quadrupole filter as the voltages on the rods are varied. There are two methods: varying w and holding U and V constant, or varying U and V (U/V) fixed for a constant w.

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