Matrix-Assisted Laser Desorption/Ionization Analysis of Non-Covalent Complexes: Fundamentals and Applications

Abstract

Mass spectrometry is now a well established and powerful method for analysing the structure of biomolecules and more recently their non-covalent interactions. It is based on two soft ionization techniques, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI), which allow to produce biomolecule ions in gas phase with a very high efficiency for a subsequent analysis in the mass analyser. The high sensitivity and the high precision of modern mass spectrometry were first applied to elucidate the primary structure of proteins in the so-called proteomic area. It is widely used in biological and medical sciences. The new challenge for the mass spectrometrist is to decipher the quaternary structure of biomolecules by preserving into the gas phase the weak interactions that exist between molecules in solution. In this review, we will focus on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for studying the non-covalent associations. Keeping in mind that the weak interactions between partners must be preserved from the solution into the gas phase, we will describe the critical parameters involved in both the desorption/ionization processes and the target preparation including the incorporation of the non-covalent complex into the matrix crystals. Various examples will be presented showing that weak interactions can survive the entire MALDI process allowing the direct detection of intact complexes. However, all these weak interactions cannot be always preserved from the cell to the mass spectrometer. Specific methodologies have been developed to get insights of these interactions. Most of them will be presented in this review.

A study of noncovalent protein complexes by matrix-assisted laser desorption/ionization

“…The later approach, which uses aqueous solution at physiological pH, more specifically aqueous solution of sinapinic acid with ammonium citrate adjusted to pH 7 with ammonium hydroxide, is very effective for the study of noncovalent protein-protein interactions by MALDI as subsequently shown. This sample preparation method gives very homogeneous analyte distribution, and the simple "dried-droplet" was used and found to be sufficient to produce spectra of complexes [3]. The results for three protein complexes are summarized here.…”

“…The laser desorption process itself may also dissociate some of the noncovalent complexes. Nevertheless, noncovalent complexes have been studied by MALDI with some success [3,4].…”

Noncovalent complexes between DNA and basic polypeptides or polyamines by MALDI-TOF

“…Formation of aggregates in the gas-phase during MALDI process is a well-known phenomenon [28]. So, when studying noncovalent complexes between DNA and polybasic compounds, great care must be taken to be sure that observed complexes pre-exist in solution and are not formed in the gas phase.…”

“…Another problem, shared with the ESI technique, is the possible formation in the gas phase of aggregates that do not reflect the in-solution species (leading to false positives). However, several works have shown that great care taken in sample preparation allowed the transfer of intact complexes from the solution to the gas phase via matrix crystals [12].…”

Detection of nucleic acid-nuclear hormone receptor complexes with mass spectrometry

“…Since the introduction of soft ionization methods, MS has become a valuable technique for characterizing noncovalent complexes. Usually, electrospray ionization (ESI) [15] or nanoelectrospray (nanoESI) mass spectrometry is preferred over matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) [16,17] for studying noncovalent complexes, such as protein-protein, proteinligand, protein-DNA, or DNA-DNA complexes. This is mainly because ESI is able to spray "native-like" aqueous solutions [18,19].…”