On the Primary Ionization Mechanism(s) in Matrix-Assisted Laser Desorption Ionization

MALDI Mass Spectrometry on High-Density Droplet Arrays: Matrix Deposition, Selective Removal, and Recrystallization

High-density droplet arrays are emerging as a powerful tool for high-throughput bioanalytical applications. These arrays are formed of thousands of nanoliter droplets, which can be analyzed by various optical and spectroscopic methods as well as label-free matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). However, special precautions are required for the massive number of small droplets, particularly in the deposition of matrix compounds. Here, we introduce a new workflow for the analytical preparation of an array comprising 6048 droplets, which significantly improves the intensity of the MALDI-MS signals. We deposited matrix compounds in a custom-made sublimation chamber followed by a recrystallization step to achieve significant signal intensity increases for three model proteins with low, medium, and large masses, respectively. Furthermore, selective removal of the matrix before recrystallization enhanced the spatial resolution and increased the signal intensity by an average of 57%. This method can be easily standardized and upscaled for the preparation of an even larger number of droplets per array for MS analysis.

Peptide-Based Mass Spectrometry for the Investigation of Protein Complexes

In the last two decades, biological mass spectrometry has become the gold standard for the identification of proteins in biological samples. The technological advancement of mass spectrometers and the development of methods for ionization, gas phase transfer, peptide fragmentation as well as for acquisition of high-resolution mass spectrometric data marked the success of the technique. This chapter introduces peptide-based mass spectrometry as a tool for the investigation of protein complexes. It provides an overview of the main steps for sample preparation starting from protein fractionation, reduction, alkylation and focus on the final step of protein digestion. The basic concepts of biological mass spectrometry as well as details about instrumental analysis and data acquisition are described. Finally, the most common methods for data analysis and sequence determination are summarized with an emphasis on its application to protein-protein complexes.

Scalable Synthesis of Crystalline One-Dimensional Carbon Nanothreads through Modest-Pressure Polymerization of Furan

Carbon nanothreads, which are one-dimensional sp³-rich polymers, combine high tensile strength with flexibility owing to subnanometer widths and diamond-like cores. These extended carbon solids are constructed through pressure-induced polymerization of sp² molecules such as benzene. Whereas a few examples of carbon nanothreads have been reported, the need for high onset pressures (≥17 GPa) to synthesize them precludes scalability and limits scope. Herein, we report the scalable synthesis of carbon nanothreads based on molecular furan, which can be achieved through ambient temperature pressure-induced polymerization with an onset reaction pressure of only 10 GPa due to its lessened aromaticity relative to other molecular precursors. When slowly compressed to 15 GPa and gradually decompressed to 1.5 GPa, a sharp 6-fold diffraction pattern is observed in situ, indicating a well-ordered crystalline material formed from liquid furan. Single-crystal X-ray diffraction (XRD) of the reaction product exhibits three distinct d-spacings from 4.75 to 4.9 Å, whose size, angular spacing, and degree of anisotropy are consistent with our atomistic simulations for crystals of furan nanothreads. Further evidence for polymerization was obtained by powder XRD, Raman/IR spectroscopy, and mass spectrometry. Comparison of the IR spectra with computed vibrational modes provides provisional identification of spectral features characteristic of specific nanothread structures, namely syn, anti, and syn/anti configurations. Mass spectrometry suggests that molecular weights of at least 6 kDa are possible. Furan therefore presents a strategic entry toward scalable carbon nanothreads.

Synthesis and Matrix Properties of α-Cyano-5-phenyl-2,4-pentadienic Acid (CPPA) for Intact Proteins Analysis by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

The effectiveness of a synthesized matrix, α-cyano-5-phenyl-2,4-pentadienic acid (CPPA), for protein analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in complex samples such as foodstuff and bacterial extracts, is demonstrated. Ultraviolet (UV) absorption along with laser desorption/ionization mass spectrometry (LDI-MS) experiments were systematically conducted in positive ion mode under standard Nd:YLF laser excitation with the aim of characterizing the matrix in terms of wavelength absorption and proton affinity. Besides, the results for standard proteins revealed that CPPA significantly enhanced the protein signals, reduced the spot-to-spot variability and increased the spot homogeneity. The CPPA matrix was successful employed to investigate intact microorganisms, milk and seed extracts for protein profiling. Compared to conventional matrices such as sinapinic acid (SA), α-cyano-4-hydroxycinnamic acid (CHCA) and 4-chloro-α-cyanocinnamic acid (CClCA), CPPA exhibited better signal-to-noise (S/N) ratios and a uniform response for most examined proteins occurring in milk, hazelnut and in intact bacterial cells of E. coli. These findings not only provide a reactive proton transfer MALDI matrix with excellent reproducibility and sensitivity, but also contribute to extending the battery of useful matrices for intact protein analysis.

Complementarity of Matrix- and Nanostructure-Assisted Laser Desorption/Ionization Approaches

In recent years, matrix-assisted laser desorption/ionization (MALDI) has become the main tool for the study of biological macromolecules, such as protein nano-machines, especially in the determination of their molecular masses, structure, and post-translational modifications. A key role in the classical process of desorption and ionization of the sample is played by a matrix, usually a low-molecular weight weak organic acid. Unfortunately, the interpretation of mass spectra in the mass range of below m/z 500 is difficult, and hence the analysis of low molecular weight compounds in a matrix-assisted system is an analytical challenge. Replacing the classical matrix with nanomaterials, e.g., silver nanoparticles, allows improvement of the selectivity and sensitivity of spectrometric measurement of biologically important small molecules. Nowadays, the nanostructure-assisted laser desorption/ionization (NALDI) approach complements the classic MALDI in the field of modern bioanalytics. In particular, the aim of this work is to review the recent advances in MALDI and NALDI approaches.

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry: Mechanistic Studies and Methods for Improving the Structural Identification of Carbohydrates

Although matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is one of the most widely used soft ionization methods for biomolecules, the lack of detailed understanding of ionization mechanisms restricts its application in the analysis of carbohydrates. Structural identification of carbohydrates achieved by MALDI mass spectrometry helps us to gain insights into biological functions and pathogenesis of disease. In this review, we highlight mechanistic details of MALDI, including both ionization and desorption. Strategies to improve the ion yield of carbohydrates are also reviewed. Furthermore, commonly used fragmentation methods to identify the structure are discussed.

"Uphill" cation transport: A bioinspired photo-driven ion pump

Biological ion pumps with active ionic transport properties lay the foundation for many life processes. However, few analogs have been produced because extra energy is needed to couple to this "uphill" process. We demonstrate a bioinspired artificial photo-driven ion pump based on a single polyethylene terephthalate conical nanochannel. The pumping process behaving as an inversion of zero-volt current can be realized by applying ultraviolet irradiation from the large opening. The light energy can accelerate the dissociation of the benzoic acid derivative dimers existing on the inner surface of nanochannel, which consequently produces more mobile carboxyl groups. Enhanced electrostatic interaction between the ions traversing the nanochannel and the charged groups on the inner wall is the key reason for the uphill cation transport behavior. This system creates an ideal experimental and theoretical platform for further development and design of various stimuli-driven and specific ion-selective bioinspired ion pumps, which anticipates wide potential applications in biosensing, energy conversion, and desalination.

Matrix-assisted laser desorption/ionization, nanostructure-assisted laser desorption/ionization and carbon nanohorns in the detection of antineoplastic drugs. 1. The cases of irinotecan, sunitinib and 6-alpha-hydroxy paclitaxel

The development of surface-assisted laser desorption/ionization (SALDI) methodologies in mass spectrometry allows, in principle, the development of new analytical approaches to qualitative and quantitative measurements on small molecules. Some of these methods have been applied to characterize two antineoplastic drugs: irinotecan (1) and sunitinib (2), and also 6-α-hydroxy-paclitaxel (3), the main metabolite of paclitaxel. Three different SALDI approaches have been tested employing nanostructure- assisted laser desorption/ionization (NALDI), carbon nanohorns (NHs) and carbon nanohorns covered by liquid additives. The results so obtained have been compared to those observed under matrix-assisted laser desorption/ionization (MALDI) conditions. Compounds 1 and 2 show the easy formation of protonated molecular species under all the experimental conditions, but the highest absolute intensity was achieved by NALDI. On the contrary, ionic species of low intensity are present for 3, among which are those that exhibit the highest intensity caused by [M+K](+) ions. After a critical evaluation of the obtained data, the linear response of the [M+H](+) ion intensity of 1 versus different deposited sample amounts was investigated, and the best results (R(2) = 0.9889) were obtained under MALDI conditions. The analysis of plasma samples spiked with 1 showed, again, that the MALDI approach was the best one (R(2) = 0.9766). The failure of NALDI measurements could be rationalized by the presence of ion suppression effects.

Chemical aspects of the primary ionization mechanisms in matrix-assisted laser desorption ionization

It has been proposed that the primary ionization mechanism occurring in matrix-assisted laser desorption ionization (MALDI) experiments originates from the presence, in the solid-state matrix-analytes sample, of matrix dimers. These species are formed by the interaction of carboxylic groups present in the matrix molecules with the formation of strong hydrogen bonds. Theoretical calculations proved that the laser irradiation of these structures leads to one or two H-bridge cleavages, giving rise to an "open" dimer structure or to disproportionation with the formation of MH(+) and [M-H](-) species. The ions so formed can be considered highly effective in their reaction with analyte ions, leading to their protonation (or deprotonation). To achieve further evidence for these proposals, in the present study the energetics of the reactions of ions from different aromatic carboxylic acids with two amino acids (glycine and lysine) and three multipeptides (gly-gly, gly-gly-gly and gly-gly-gly-gly) was investigated. The lowest ∆G values were obtained for 2,5- dihydroxybenzoic acid, widely employed as the MALDI matrix. Also, for p-nitrobenzoic acid the reaction is slightly exothermic, while for the other aromatic carboxylic acids derivatives positives values of ∆G are present.

Why do the abundances of ions generated by MALDI look thermally determined?

In a previous study (J. Mass Spectrom. 48, 299-305, 2013), we observed that the abundance of each ion in a matrix-assisted laser desorption ionization (MALDI) spectrum looked thermally determined. To find out the explanation for the phenomenon, we estimated the ionization efficiency and the reaction quotient (QA) for the autoprotolysis of matrix, M + M → [M + H](+) + [M - H](-), from the temperature-controlled laser desorption ionization spectra of α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB). We also evaluated the equilibrium constants (KA) for the autoprotolysis at various temperatures by quantum chemical calculation. Primary ion formation via various thermal models followed by autoprotolysis-recombination was compatible with the observations. The upper limit of the effective temperature of the plume where autoprotolysis-recombination occurs was estimated by equating QA with the calculated equilibrium constant. Figure ᅟ