Overview of the Ionization Techniques

The instruments in the facility offer the most common ionization techniques. This page helps to understand how the various ionization sources work and thus to select the most appropriate one for the samples.

Atmospheric Pressure Chemical Ionization (APCI) is a soft ionization technique used for organic compounds with medium to high polarity. The dissolved sample is introduced into the APCI source. The solvent is evaporated and the sample passes through a corona discharge where reagent ions are formed from the solvent molecules and the nitrogen gas. These ions react with the analyte. The relative gas phase acidity of the reagent ions and the analyte molecules play important roles in the APCI process. Positive ions are formed by proton adduction [M+H]⁺ and negative ions by proton abstraction [M-H]^-; cation or anion radicals ([M]^.+, [M]^.-) are also sometimes observed. Several fragment ions are usually observed. The molecular weight range is up to ~2 000 u.

Electron Ionization (EI) is used for relatively volatile samples that are insensitive to heat and have rather low molecular weight. During the ionization process the analyte molecules interact with a beam of energetic electrons (70 eV). The molecules lose electrons forming a radical cations; a portion of them further fragment to remove the excess internal energy. As the spectra usually contain many fragment-ion peaks, they are very useful for structure characterization and identification. Searching a database may sometimes identify unknown compounds. The NIST mass spectral library contains mass spectra of more than 160 000 compounds. The molecular weight range is up to ~800 u.

Electrospray Ionization (ESI) is a very soft ionization technique used for small organic molecules as well as for high molecular weight biomolecules such as peptides, proteins, carbohydrates, or oligonucleotides. The sample in solution is passed through a capillary held at high potential (a few kV). The liquid at the tip of the capillary blows apart into a cloud of tiny, highly charged droplets, which further repeatedly shrink and blow to eventually form the ions. For small molecules either [M+H]⁺ or [M-H]^- ions are formed. Because of alkali metal impurities, [M+Na]⁺ ions are observed. Molecules with higher masses usually produce a series of multiply charged ions. No or few fragments are usually observed. The molecular weight range is up to ~200 000 u.

Matrix-Assisted Laser Desorption/Ionisation (MALDI) is a soft ionization technique suitable for a wide range of biologically important molecules as well as for other compounds, such as synthetic polymers, large organic molecules, or organometallic complexes. Most often MALDI is used for analyzing proteins or protein digests.The sample is mixed with a matrix solution and allowed to co-crystallize on a target plate. Laser (usually nitrogen laser 337 nm) is fired at the target, and the absorbed laser energy desorbs the sample and matrix from the surface. The matrix also serves as a proton donor and acceptor, acting to ionize the analyte. A voltage is applied to the target plate to accelerate the analyte ions towards a mass analyzer. The choice of matrix is crucial for successful MALDI analysis. The analyte molecules are usually ionized by a simple protonation or cationization leading to the formation of [M+H]⁺, [M+Na]⁺ etc. in positive ion mode or by deprotonation in negative ion mode ([M-H]^-). MALDI has tendency to produce singly-charged ions even with very large molecules, however, some multiply charged species, or singly charged dimers and trimers can also be formed. The molecular weight range is up to ~500 000 u.