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Methods of ionization

There are numerous ways to ionize things. We are set up to do two, which are complementary and between them cover most sorts of sample.

AP-ESI Atmospheric pressure electro-spray ionization	This method is good for all metabolites that would normally already have a charge in solution. It is a very gentle method, also well suited to protein work. Multiple charges are possible. Since the mass spec measures mass per charge, multiple charges mean that you can measure very large things without going over the largest-mass limit of the detector (usually about 2000 amu).
APCI Atmospheric pressure chemical ionization	This method is a bit more ferocious and can ionize things that are less-polar and normally not ionized well by ES. It tends to be less suitable for things that already would be ionized in solution. Usually ions are singly-charged.

GC-MS uses electron ionization or chemical ionization at low pressure. Electron ionization is very different to the LC-MS forms of ionization. GC-MS requires volatility, but an electron beam can ionize almost anything. In contrast, even for APCI, the target molecule has to have at least a little polarity; some easily ionizable group. Fortunately few biological chemicals are utterly free of polar groups.

After ionization, the mass spec must get the ions into a vacuum, then separate them by mass, and detect them.