Archive for April 20th, 2012

GC-MS and LC-MS typically use totally different mechanisms for ionisation. In GC-MS the sample is usually ionised directly (Electron Impact, EI), or indirectly (Chemical Ionization, CI) by an electron beam. The high-energy electrons cause the formation of free radical ions. These are ions because they’ve lost an electron, so they have the same mass as the parent, but an odd number of electrons.

In fact the electron beam is often energetic enough to cause substantial fragmentation. The fragments are also free radicals, and form the “fingerprint” that is used in confirmation of identity. This fingerprint is compared with library fingerprints; NIST is probably the most widely used library.

An example might be Aspirin, acetyl-salicylate. By EI in GC-MS, this has a tiny peak at 180amu, corresponding to the molecular ion (free radical; the MWt of acetyl salicylate is 180Da). But the major peaks are all fragments: 120, 138, 92, 43amu, and many others.

In contrast, the spectrum below is acetyl-salicylate measured in LC-MS, using electrospray ionisation, ESI (in negative mode):

Notice that the major ion is now 179amu. This is a pseudomolecular ion, formed by loss of H+. This is quite typical in electrospray: the major ion is formed without fragmentation (unlike EI), and it is formed by loss of H+ in negative mode, or by gain of H+, Na+, or some other ion (ammonium and potassium are quite common) in positive mode. Very often in positive mode, one sees a mixture. Peaks 22amu apart nearly always mean the H+ and Na+ ions of the same thing.

Acetyl salicylate is a very easily fragmented molecule, so two fragments are still visible even under the mild conditions of ESI. These are the ions at 137 and 93amu. Unfortunately ESI collision-induced fragmentations are often not very peak-rich, so they are often not such good “fingerprints” as EI spectra. They can also vary with instrument and conditions.

Notice also the peaks at 225 and 381amu. These are adducts. Unfortunately analytes often associate weakly in the spray-chamber in ESI, and then appear as adducts of two things together. 225amu is probably a formate acid adduct of acetyl salicylate (46+179), and 381 is a sodium dimer (179+179+23; notice there is still a single negative charge). Adducts are most problematic at high concentrations.


Download (gift from Dr. Lionel Hill, John Innes Centre, UK) :

1. Modul Training HPLC

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