Intro to MS

Introduction to MS

Mass spectrometry begins with an ionization process.  A molecule M is ionized by either electron ionization (EI) or chemical ionization (CI) methods.  The resulting unstable radical cation (M^+.) is referred to as the molecular ion.  The molecular ion undergoes various fragmentation processes to form daughter ions, radicals and or radical cations (D).  Electron ionization or EI is by far the most commonly used ionization technique.  Chemical ionization is a milder technique resulting in less fragmentation.   

The molecular ion and those daughter fragments that are ions (must have charge) are then detected.  A mass spectra shows the mass (m/z) of the ions on the x-axis and the abundance of these ions on the y-axis.  The m is the mass of the ion while z is the charge.  Most of the time z=1 so the m/z correspoonds to the atomic mass of the ion.  The largest peak is called the base peak and it doesn’t necessarily correspond to the molecular ion peak.  The larger a peak is the more stable (more abundant) the ions.

For example in the following spectra of methanol, the molecular ion peak is visible at m/z=32, which corresponds to the molecular weight of CH₃OH.  The base peak or most abundant peak is the m/z=31 peak.  The peaks at m/z= 31, 29 and 15 etc are daughter ions resulting from fragmentation.

Ionization

When a molecule is ionized by EI, usually the least stable electron is lost.  These are typically electrons in HOMO's.  When heteroatoms are present its their non-bonded electron pairs that lie in the HOMO and these are the electrons most readily lost.  In these cases we can indicate where the electron was lost from.  However with most hydrocarbons like alkanes, we can not attribute the lost electron to any specific lone pairs or bonds.   The following scheme illustrates ionization of some common functional groups.  These radical cations correspond to the molecular ion (or parent ion) peak and are the starting point when considering fragmentation processes.