The 2nd theory - assumes that the analyte is evapourated into the gas phase as neutral and gets gas phase protonated by the matrix.
The two theories have in common that there are a certain number of neutral matrix or matrix-analyte cluster present in the gas phase. These neutrals are lost within the MS but still have the potential to be ionized and therefore limit the ion yield.
MALDI 2 tries to target exactly these neutrals, which require more energy to ionize or to re-ionize, by inducing a second MALDI ionization.
To minimize spatial expansion of the ion plume source parameter, such as pressure, laser wavelength, beam focus and the timing are really important to make this technique work. Since spatial expansion is still present and therefore different starting conditions for the MALDI ions orthogonal TOF is highly benefical for mass analysis.
MALDI 2 increases sensitivity for lipids by two orders of magnitude.
http://science.sciencemag.org/content/early/2015/03/04/science.aaa1051.full
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