Imaging of noncovalent complexes by MALDI-MS

Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes

Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.

Improving the analyte ion signal in matrix-assisted laser desorption/ionization imaging mass spectrometry via electrospray deposition by enhancing incorporation of the analyte in the matrix

RATIONALE

Matrix-assisted laser desorption/ionization (MALDI) is widely used as the ionization method in high-resolution chemical imaging studies that seek to visualize the distribution of analytes within sectioned biological tissues. This work extends the use of electrospray deposition (ESD) to apply matrix with an additional solvent spray to incorporate and homogenize analyte within the matrix overlayer.

METHODS

Analytes and matrix are sequentially and independently applied by ESD to create a sample from which spectra are collected, mimicking a MALDI imaging mass spectrometry (IMS) experiment. Subsequently, an incorporation spray consisting of methanol is applied by ESD to the sample and another set of spectra are collected. The spectra prior to and after the incorporation spray are compared to evaluate the improvement in the analyte signal.

RESULTS

Prior to the incorporation spray, samples prepared using α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB) as the matrix showed low signal while the sample using sinapinic acid (SA) initially exhibited good signal. Following the incorporation spray, the sample using SA did not show an increase in signal; the sample using DHB showed moderate gain factors of 2-5 (full ablation spectra) and 12-336 (raster spectra), while CHCA samples saw large increases in signal, with gain factors of 14-172 (full ablation spectra) and 148-1139 (raster spectra).

CONCLUSIONS

The use of an incorporation spray to apply solvent by ESD to a matrix layer already deposited by ESD provides an increase in signal by both promoting incorporation of the analyte within and homogenizing the distribution of the incorporated analyte throughout the matrix layer. Copyright © 2017 John Wiley & Sons, Ltd.

Pre-Assembly of Near-Infrared Fluorescent Multivalent Molecular Probes for Biological Imaging

A programmable pre-assembly method is described and shown to produce near-infrared fluorescent molecular probes with tunable multivalent binding properties. The modular assembly process threads one or two copies of a tetralactam macrocycle onto a fluorescent PEGylated squaraine scaffold containing a complementary number of docking stations. Appended to the macrocycle periphery are multiple copies of a ligand that is known to target a biomarker. The structure and high purity of each threaded complex was determined by independent spectrometric methods and also by gel electrophoresis. Especially helpful were diagnostic red-shift and energy transfer features in the absorption and fluorescence spectra. The threaded complexes were found to be effective multivalent molecular probes for fluorescence microscopy and in vivo fluorescence imaging of living subjects. Two multivalent probes were prepared and tested for targeting of bone in mice. A pre-assembled probe with 12 bone-targeting iminodiacetate ligands produced more bone accumulation than an analogous pre-assembled probe with six iminodiacetate ligands. Notably, there was no loss in probe fluorescence at the bone target site after 24 h in the living animal, indicating that the pre-assembled fluorescent probe maintained very high mechanical and chemical stability on the skeletal surface. The study shows how this versatile pre-assembly method can be used in a parallel combinatorial manner to produce libraries of near-infrared fluorescent multivalent molecular probes for different types of imaging and diagnostic applications, with incremental structural changes in the number of targeting groups, linker lengths, linker flexibility, and degree of PEGylation.

Applying mass spectrometry to study non-covalent biomolecule complexes

Non-covalent interactions are essential for the structural organization of biomacromolecules and play an important role in molecular recognition processes, such as the interactions between proteins, glycans, lipids, DNA, and RNA. Mass spectrometry (MS) is a powerful tool for studying of non-covalent interactions, due to the low sample consumption, high sensitivity, and label-free nature. Nowadays, native-ESI MS is heavily used in studies of non-covalent interactions and to understand the architecture of biomolecular complexes. However, MALDI-MS is also becoming increasingly useful. It is challenging to detect the intact complex without fragmentation when analyzing non-covalent interactions with MALDI-MS. There are two methodological approaches to do so. In the first approach, different experimental and instrumental parameters are fine-tuned in order to find conditions under which the complex is stable, such as applying non-acidic matrices and collecting first-shot spectra. In the second approach, the interacting species are "artificially" stabilized by chemical crosslinking. Both approaches are capable of studying non-covalently bound biomolecules even in quite challenging systems, such as membrane protein complexes. Herein, we review and compare native-ESI and MALDI MS for the study of non-covalent interactions.