Indirect study of non-covalent protein complexes by MALDI mass spectrometry: Origins, advantages, and applications of the "intensity-fading" approach

Structural Phylogenetics with Protein Mass Spectrometry: A Proof-of-Concept

It is demonstrated, for the first time, that a mass spectrometry approach (known as phylonumerics) can be successfully implemented for structural phylogenetics investigations to chart the evolution of a protein's structure and function. Illustrated for the compact globular protein myoglobin, peptide masses produced from the proteolytic digestion of the protein across animal species generate trees congruent to the sequence tree counterparts. Single point mutations calculated during the same mass tree building step can be followed along interconnected branches of the tree and represent a viable structural metric. A mass tree built for 15 diverse animal species, easily resolve the birds from mammal species, and the ruminant mammals from the remainder of the animals. Mutations within helix-spanning peptide segments alter both the mass and structure of the protein in these segments. Greater evolution is found in the B-helix over the A, E, F, G and H helices. A further mass tree study, of six more closely related primate species, resolves gorilla from the other primates based on a P22S mutation within the B-helix. The remaining five primates are resolved into two groups based on whether they contain a glycine or serine at position 23 in the same helix. The orangutan is resolved from the gibbon and siamang by its G-helix C110S mutation, while homo sapiens are resolved from chimpanzee based on the Q116H mutation. All are associated with structural perturbations in such helices. These structure altering mutations can be tracked along interconnecting branches of a mass tree, to follow the protein's structure and evolution, and ultimately the evolution of the species in which the proteins are expressed. Those that have the greatest impact on a protein's structure, its function, and ultimately the evolution of the species, can be selectively tracked or monitored.

Analyzing noncovalent interactions between notoginseng saponins and lysozyme by deposition scanning intensity fading MALDI-TOF mass spectrometry

Analysis of noncovalent interactions between natural products and proteins is important for rapid screening of active ingredients and understanding their pharmacological activities. In this work, the intensity fading MALDI-TOF mass spectrometry (IF-MALDI-MS) method with improved reproducibility was implemented to investigate the binding interactions between saponins from Panax notoginseng and lysozyme. The benchmark IF-MALDI-MS experiment was established using N,N',N″-triacetylchitotriose-lysozyme as a model system. The reproducibility of ion intensities in IF-MALDI-MS was improved by scanning the whole sample deposition with a focused laser beam. The relative standard deviation (RSD) of deposition scanning IF-MALDI-MS is 5.7%. Similar decay trends of the relative intensities of notoginseng saponins against increasing amounts of lysozyme were observed for all six notoginseng saponins. The half-maximal fading concentration (FC50) was calculated to quantitatively characterize the binding affinity of each ligand based on the decay curve. According to the FC50 values obtained, the binding affinities of the six notoginseng saponins were evaluated in the following order: notoginsenoside S > notoginsenoside Fc > ginsenoside Rb1 > ginsenoside Rd > notoginsenoside Ft1 > ginsenoside Rg1. The binding order was in accordance with molecular docking studies, which showed hydrogen bonding might play a key role in stabilizing the binding interaction. Our results demonstrated that deposition scanning IF-MALDI-MS can provide valuable information on the noncovalent interactions between ligands and proteins.

25 Years Responding to Respiratory and Other Viruses with Mass Spectrometry

This review article presents the development and application of mass spectrometry (MS) approaches, developed in the author's laboratory over the past 25 years, to detect; characterise, type and subtype; and distinguish major variants and subvariants of respiratory viruses such as influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All features make use of matrix-assisted laser desorption ionisation (MALDI) mass maps, recorded for individual viral proteins or whole virus digests. A MALDI-based immunoassay in which antibody-peptide complexes were preserved on conventional MALDI targets without their immobilisation led to an approach that enabled their indirect detection. The site of binding, and thus the molecular antigenicity of viruses, could be determined. The same approach was employed to study antivirals bound to their target viral protein, the nature of the binding residues, and relative binding affinities. The benefits of high-resolution MS were exploited to detect sequence-conserved signature peptides of unique mass within whole virus and single protein digests. These enabled viruses to be typed, subtyped, their lineage determined, and variants and subvariants to be distinguished. Their detection using selected ion monitoring improved analytical sensitivity limits to aid the identification of viruses in clinical specimens. The same high-resolution mass map data, for a wide range of viral strains, were input into a purpose-built algorithm (MassTree) in order to both chart and interrogate viral evolution. Without the need for gene or protein sequences, or any sequence alignment, this phylonumerics approach also determines and displays single-point mutations associated with viral protein evolution in a single-tree building step.

Substrate-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry of Some Small Biomolecules Using TiO2-Nanotubes: The Effect of Nanotube Diameter and Salt Addition

Substrate-assisted laser desorption/ionization (SALDI) is a kind of soft ionization method that is most suitable for the analysis of low molecular weight analytes when it is coupled with a time-of-flight mass spectrometer. Unlike the conventional matrix-assisted laser desorption/ionization, there is no interference in the SALDI with matrices for the low mass analyte peaks (m/z < 700). The focus of this work is to develop substrates based on nanomaterials to obtain higher sensitivity, better reproducibility, and easier preparation. The mass spectra of some small molecules (capecitabine, hemin, methadone, noscapine, oxycodone, thebaine, malathion, chlorpyrifos, ethion, permethrin, and phosalone) deposited on the TiO₂-nanotube (TiO₂-NTs) plate by the SALDI-TOF-MS technique are reported. The nanotubes are synthesized in different diameter sizes of nanotubes via the anodizing method. The intensity of the analyte peaks and the softness of ionization are optimized by varying the diameter of nanotubes and adding relevant alkali salts to the analytes. In addition, the reproducibility of the signal intensity of analytes is optimized by changing the surface hydrophilicity of the TiO₂-NT plate.

Native Mass Spectrometry Coupled to Spectroscopic Methods to Investigate the Effect of Soybean Isoflavones on Structural Stability and Aggregation of Zinc Deficient and Metal-Free Superoxide Dismutase

The deficiency or wrong combination of metal ions in Cu, Zn-superoxide dismutase (SOD1), is regarded as one of the main factors causing the aggregation of SOD1 and then inducing amyotrophic lateral sclerosis (ALS). A ligands-targets screening process based on native electrospray ionization ion mobility mass spectrometry (ESI-IMS-MS) was established in this study. Four glycosides including daidzin, sophoricoside, glycitin, and genistin were screened out from seven soybean isoflavone compounds and were found to interact with zinc-deficient or metal-free SOD1. The structure and conformation stability of metal-free and zinc-deficient SOD1 and their complexes with the four glycosides was investigated by collision-induced dissociation (CID) and collision-induced unfolding (CIU). The four glycosides could strongly bind to the metal-free and copper recombined SOD1 and enhance the folding stability of these proteins. Additionally, the ThT fluorescence assay showed that these glycosides could inhibit the toxic aggregation of the zinc-deficient or metal-free SOD1. The competitive interaction experiments together with molecular docking indicate that glycitin, which showed the best stabilizing effects, binds with SOD1 between β-sheet 6 and loop IV. In short, this study provides good insight into the relationship between inhibitors and different SOD1s.

Mass Spectrometry as a Crucial Analytical Basis for Omics Sciences

This review is devoted to the consideration of mass spectrometric platforms as applied to omics sciences. The most significant attention is paid to omics related to life sciences (genomics, proteomics, meta-bolomics, lipidomics, glycomics, plantomics, etc.). Mass spectrometric approaches to solving the problems of petroleomics, polymeromics, foodomics, humeomics, and exosomics, related to inorganic sciences, are also discussed. The review comparatively presents the advantages of various principles of separation and mass spectral techniques, complementary derivatization, used to obtain large arrays of various structural and quantitative information in the mentioned omics sciences.

A Molecular Immunoproteomics Approach to Assess the Viral Antigenicity of Influenza

New surveillance methods employing mass spectrometry (MS) have been developed to characterize the influenza virus and, by extension, other biopathogens at the molecular level. The structure and antigenicity of protein antigens on the surface of the viral capsid are screened in a single step employing the immunoproteomics MS-based approach. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) coupled to gel electrophoresis is used both to identify viral antigens and screen their antigenicity. Evidence that antigen-antibody complexes, and protein complexes more generally, can survive on conventional MALDI targets has allowed both the primary structure and antigenicity of viral strains to be rapidly screened and protein epitopes to be identified with molecular precision. The approach should aid in future screening of the virus and assist in the development of immunogenic peptide constructs as alternative treatments to vaccination over the whole inactivated virus. The assay adds to the repertoire of mass spectrometric approaches for examining antigen-antibody interactions, in particular, and protein complexes, in general, without the need to immobilize, tag, or recover either component.

Comprehensive investigation of in-vivo ingredients and action mechanism of iridoid extract from Gardeniae Fructus by liquid chromatography combined with mass spectrometry, microdialysis sampling and network pharmacology

Gardeniae Fructus is a widely used Traditional Chinese Medicines in treating various diseases. However, the absorbed components and metabolites of its main bioactive iridoid ingredients from iridoid extract of the fruits of Gardeniae Fructus in rat plasma need further study. In this study, a systematic method based on ultra-performance liquid chromatography-quadrupole-time-of-flight/mass spectrometry (UPLC-Q-TOF/MS) technique was developed to speculate the absorbed components and metabolites of iridoid extract in rat plasma after oral administration. A total of 19 compounds, including 9 prototype components and 10 metabolites were identified in plasma. 5 metabolites containing 4 new metabolites (M1, M2, M7, M10) were tentatively determined in rat plasma. Besides, Microdialysis-intensity-fading mass spectrometry (MD-IF-MS) method was originally employed to reveal the binding affinities with α-glucosidase for in-vivo prototype components and their metabolites. Finally, the absorbed constituents and the corresponding target proteins were used to generate compound-target network to find the related diseases and action pathways by a network pharmacology method. The results provide useful information for further study of pharmacology and in vivo mechanism of action of iridoid extract from the fruits of Gardeniae Fructus.

Systematic study on metabolism and activity evaluation of Radix Scutellaria extract in rat plasma using UHPLC with quadrupole time-of-flight mass spectrometry and microdialysis intensity-fading mass spectrometry

Radix Scutellaria is a widely used traditional Chinese medicine in the treatment of various diseases. However, the activities of the absorbed components and metabolites of its main flavones in rat plasma need further investigation. In this study, a systematic method based on ultra-high performance liquid chromatography with quadruple time-of-flight mass spectrometry was developed to speculate the absorbed components and metabolites of the main flavonoids in Radix Scutellaria extract in rat plasma sample after oral administration of the extract. Twelve compounds, including four prototype components and eight metabolites, were confirmed in drug-containing plasma. In these metabolites, five were originally detected in rat plasma. The possible metabolic pathways of these polyhydroxy flavones in vivo were described and clarified. Microdialysis with intensity-fading mass spectrometry was originally employed to investigate the binding affinities of the absorbed components and metabolites with α-glucosidase. The order of their binding affinities was P4 > P3 > P2 > P1≥M5 > M3 > M1. The research result is helpful to deepen the understanding of the absorbed components and metabolic pathways of main flavones from Radix Scutellaria, and provide a new approach to screen potential inhibitors from in vivo components originated from Chinese herb.

Nanomaterials as Assisted Matrix of Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for the Analysis of Small Molecules

Matrix-assisted laser desorption/ionization (MALDI), a soft ionization method, coupling with time-of-flight mass spectrometry (TOF MS) has become an indispensible tool for analyzing macromolecules, such as peptides, proteins, nucleic acids and polymers. However, the application of MALDI for the analysis of small molecules (<700 Da) has become the great challenge because of the interference from the conventional matrix in low mass region. To overcome this drawback, more attention has been paid to explore interference-free methods in the past decade. The technique of applying nanomaterials as matrix of laser desorption/ionization (LDI), also called nanomaterial-assisted laser desorption/ionization (nanomaterial-assisted LDI), has attracted considerable attention in the analysis of low-molecular weight compounds in TOF MS. This review mainly summarized the applications of different types of nanomaterials including carbon-based, metal-based and metal-organic frameworks as assisted matrices for LDI in the analysis of small biological molecules, environmental pollutants and other low-molecular weight compounds.