Advances in mass spectrometry-based multi-scale metabolomic methodologies and their applications in biological and clinical investigations

Metabolomics is a nascent field of inquiry that emerged in the late 20th century. It encompasses the comprehensive profiling of metabolites across a spectrum of organisms, ranging from bacteria and cells to tissues. The rapid evolution of analytical methods and data analysis has greatly accelerated progress in this dynamic discipline over recent decades. Sophisticated techniques such as liquid chromatograph mass spectrometry (MS), gas chromatograph MS, capillary electrophoresis MS, and nuclear magnetic resonance serve as the cornerstone of metabolomic analysis. Building upon these methods, a plethora of modifications and combinations have emerged to propel the advancement of metabolomics. Despite this progress, scrutinizing metabolism at the single-cell or single-organelle level remains an arduous task over the decades. Some of the most thrilling advancements, such as single-cell and single-organelle metabolic profiling techniques, offer profound insights into the intricate mechanisms within cells and organelles. This allows for a comprehensive study of metabolic heterogeneity and its pivotal role in multiple biological processes. The progress made in MS imaging has enabled high-resolution in situ metabolic profiling of tissue sections and even individual cells. Spatial reconstruction techniques enable the direct representation of metabolic distribution and alteration in three-dimensional space. The application of novel metabolomic techniques has led to significant breakthroughs in biological and clinical studies, including the discovery of novel metabolic pathways, determination of cell fate in differentiation, anti-aging intervention through modulating metabolism, metabolomics-based clinicopathologic analysis, and surgical decision-making based on on-site intraoperative metabolic analysis. This review presents a comprehensive overview of both conventional and innovative metabolomic techniques, highlighting their applications in groundbreaking biological and clinical studies.

Review of recent advances on the use of mass spectrometry techniques for the study of organic materials in painted artworks

The study of painted artworks using scientific methods is fundamental for understanding the techniques used in their creation and their appropriate conservation. The ethical constraints involved in the handling of, and sampling from, these objects has steered recent developments in the field of Heritage science towards a range of new non-invasive/non-destructive spectroscopic techniques capable of providing important insights into their elemental or bulk chemical compositions. Due to the inherent complexities of heritage artefacts, however, their organic components are especially difficult to study in this way and their identification and degradation pathways are thus often best investigated using mass spectrometric (MS) techniques. The versatility, sensitivity and specificity of MS techniques are constantly increasing, with technological advances pushing the boundaries of their use in this field. The progress in the past ten years in the use of MS techniques for the analysis of paint media are described in the present review. While some historical context is included, the body of the review is structured around the five most widely used or emerging capabilities offered by MS. The first pertains to the use of spatially resolved MS to obtain chemical maps of components in cross-sections, which may yield information on both inorganic and organic materials, while the second area describes the development of novel sample preparation approaches for gas chromatography (GC)-MS to allow simultaneous analysis of a variety of components. The third focuses on thermally assisted analysis (either with direct MS or coupled with GC-MS), a powerful tool for studying macromolecules requiring zero (or minimal) sample pre-treatment. Subsequently, the use of soft ionisation techniques often combined with high-resolution MS for the study of peptides (proteomics) and other macromolecules (such as oligosaccharides and triglycerides) is outlined. The fifth area covers the advances in radiocarbon dating of painting components with accelerator MS (AMS). Lastly, future applications of other MS techniques to the study of paintings are mentioned; such as direct analysis in real time MS (DART-MS) and stable isotope ratio MS (IRMS). The latter, having proven its efficiency for the study of lipids in archaeological artefacts, is envisioned to become a valuable tool for this area, whereas DART-MS is already being utilised to study the surface composition of various museum objects. Rapid technological advances, resulting in increased sensitivity and selectivity of MS techniques, are opening up new approaches for paintings analysis, overcoming the fundamental hurdle of sample size available for destructive analysis. Importantly, while the last decade has seen proteomics applications come to the fore, this review aims to emphasise the wider potential of advanced MS techniques for the study of painting materials and their conservation.

Deep Time Paleoproteomics: Looking Forward

The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.

Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics

Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics. In the decades following, proteins continued to provide essential clues on evolutionary history. While technology has continued to improve, contemporary proteomics has strayed from this larger biological context, rarely comparing species or asking how protein structure, function, and interactions have evolved. Here we recombine proteomics with molecular phylogenetics, highlighting the value of framing proteomic results in a larger biological context and how almost forgotten research, though technologically surpassed, can still generate new ideas and illuminate our work from a different perspective. Though it is infeasible to read all research published on a large topic, looking up older papers can be surprisingly rewarding when rediscovering a “gem” at the end of a long citation chain, aided by digital collections and perpetually helpful librarians. Proper literature study reduces unnecessary repetition and allows research to be more insightful and impactful by truly standing on the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/) as dataset MSV000087993.

Characterization of surface materials on African sculptures: new insights from a multi-analytical study including proteomics

Multiple analytical techniques were used to characterize materials from the surfaces of two African sculptures in the collection of the Art Institute of Chicago: a Bamana power object (boli), and a Yoruba wooden sculpture of a female figure. Surface accretions on objects such as these have received relatively little scientific attention to elucidate their composition and function, in part because they are made with complex mixtures of natural materials, which are often unfamiliar and poorly represented in the scientific literature on artists' materials. For this reason, a complement of techniques including Fourier transform infrared spectroscopy and pyrolysis gas chromatography mass spectrometry were applied, along with shotgun proteomics to better understand the nature and biological origin, down to the species level, of the proteinaceous materials. The results highlighted the presence of diverse materials including plant resins, oils, polysaccharides, and inorganic (clay or earth) compounds. In particular, mass spectrometry-based proteomics provided new insights on proteinaceous components, allowing us to identify the presence of sacrificial blood, and more specifically, blood from chicken, goat, sheep and dog. This new scientific evidence supports and supplements knowledge derived from curatorial and field work studies, and opens new doors to understanding the objects' significance and history of use.

Forensic applications of DART-MS: A review of recent literature

The need for rapid chemical analyses and new analytical tools in forensic laboratories continues to grow due to case backlogs, difficult-to-analyze cases, and identification of previously unseen materials such as new psychoactive substances. To adapt to these needs, the forensics community has been pursuing the use of ambient ionization mass spectrometry, and more specifically direct analysis in real time mass spectrometry (DART-MS), for a wide range of applications. From the inception of DART-MS forensic applications have been researched with demonstrations ranging from drugs of abuse to inorganic gunshot residue to printer inks to insect identification. This article presents a review of research demonstrating the use of DART-MS for forensically relevant samples over the past five years. To provide more context, background on the technique, sampling approaches, and data analysis methods are presented along with a discussion on the potential future and research needs of the technology.

Diagenetiforms: A new term to explain protein changes as a result of diagenesis in paleoproteomics

The term proteoform describes all combinations of change in a protein, as elucidated through intact mass proteomics. Paleoproteomic studies have begun using digestion-free and top-down techniques to access information from ancient and historical remains. However, to discuss protein changes that uniquely occur to archaeological and paleontological proteomes as the result of diagenesis (i.e., physical and chemical change imparted by burial), a novel term is needed that both addresses issues of combinatorics and distinguishes diagenetic-specific alteration. SIGNIFICANCE: The term diagenetiform provides the opportunity to communicate clearly the sets of diagenetic changes found on preserved proteins. The diagenetiform nomenclature will allow for top-down paleoproteomic studies to accurately describe the total changes detected on ancient proteins.

Rapid identification of polyamides using direct analysis in real time mass spectrometry

RATIONALE

Polyamide (PA) is the generic name of polymers synthesized by linking monomers via amide bonds, and various types of PAs with different monomer compositions are known. Distinguishing PA polymers is useful in directing monomer residual testing, product testing, and reverse engineering, but is analytically challenging and cumbersome. To simplify this, we explored the applicability of direct analysis in real time mass spectrometry (DART-MS) for screening PA polymers.

METHODS

A DART ion source coupled to a quadrupole Orbitrap (high-resolution (HR) mass spectrometer) was employed for this study. Ten types of PA polymers and four retail samples were evaluated. The DART-HRMS data for these samples, as well as the DART-MS/MS (MS² ) data for PA6 and PA66, were obtained, and their repeatability was assessed across days/calibrations, operators, and equipments.

RESULTS

Ions corresponding to the cyclic or linear monomers and oligomers of each PA polymer were detected in each DART-HR mass spectrum. Although similar DART-HR mass spectra were obtained for PA6, PA66, and PA6/PA66 (polymer blends of PA6 and PA66), their DART tandem mass spectra were completely different. The analysis was repeatable, and nearly identical DART tandem mass spectra were obtained on different days, by different operators, and with different equipment. This technique was successfully applied to commercially available samples.

CONCLUSIONS

Ten types of PA polymers were distinguished using DART-HRMS and DART-MS² , and their identification using these techniques was straightforward as the characteristic ions for each PA polymer were identified and detected. Furthermore, the spectra were obtained rapidly. Therefore, DART-HRMS can be considered an efficient screening technique for the rapid identification and differentiation of PA polymers.