Mass Spectrometry Reviews最新文献

An intricate network of protein assemblies and protein-protein interactions (PPIs) underlies nearly every biological process in living systems. The organization of these cellular networks is highly dynamic and intimately tied to the genomic and proteomic landscapes of a cell. Disruptions in normal PPIs can impair cellular functions and contribute to the development of human diseases. In recent years, targeting PPIs has emerged as an attractive strategy for drug discovery. Consequently, the identification and characterization of endogenous PPIs-those occurring naturally under physiological conditions-has become crucial for unraveling the molecular mechanisms driving human pathology and for laying the groundwork for novel diagnostics and therapeutics. Owing to numerous technological advancements, mass spectrometry (MS)-based proteomics has transformed the study of PPIs at the systems-level. This review focuses on proteomics approaches that enable the characterization of physiologically relevant endogenous interactions, spanning complex-centric to structure-centric analyses. Additionally, their applications to define native PPIs in the contexts of cancer and viral infectious diseases is highlighted.

With the increasing FDA approvals of glycoprotein-based biotherapeutics including monoclonal antibodies, cytokines, and enzyme treatments, the significance of glycosylation in modulating drug efficacy and safety becomes central. This review highlights the crucial role of mass spectrometry (MS) in elucidating the glycome of biotherapeutics that feature N- and O-glycosylation, directly addressing the challenges posed by glycosylation complexity and heterogeneity. We have detailed the advancements and application of MS technologies including MALDI-TOF MS, LC-MS, and tandem MS in the precise characterization of glycoprotein therapeutics. Emphasizing MS-based strategies for detecting immunogenic glycans and ensuring batch-to-batch consistency, this review highlights targeted approaches for glycoprotein, glycopeptide, and glycan analysis tailored to meet the stringent analytical and regulatory demands of biopharmaceutical development.

Ionization and fragmentation are at the core of mass spectrometry. But they are not necessarily separated in space, as in-source fragmentation can also occur. Here, we survey the literature published since our 2005 review on the internal energy and fragmentation in electrospray ionization sources. We present new thermometer molecules to diagnose and quantify source heating, provide tables of recommended threshold (E₀) and appearance energies (E_app) for the survival yield method, and attempt to compare the softness of a variety of ambient pressure ionization sources. The droplet size distribution and desolvation dynamics play a major role: lower average internal energies are obtained when the ions remain protected by a solvation shell and spend less time nakedly exposed to activating conditions in the transfer interface. Methods based on small droplet formation without charging can thus be softer than electrospray. New dielectric barrier discharge sources can gas-phase ionize small molecules while conferring barely more internal energy than electrospray ionization. However, the tuning of the entire source interface often has an even greater influence on ion internal energies and fragmentation than on the ionization process itself. We hope that this review will facilitate further research to control and standardize in-source ion activation conditions, and to ensure the transferability of data and research results in mass spectrometry.

Mass spectrometry (MS) has become a critical tool in the characterization of covalently modified nucleic acids. Well-developed bottom-up approaches, where nucleic acids are digested with an endonuclease and the resulting oligonucleotides are separated before MS and MS/MS analysis, provide substantial insight into modified nucleotides in biological and synthetic nucleic. Top-down MS presents an alternative approach where the entire nucleic acid molecule is introduced to the mass spectrometer intact and then fragmented by MS/MS. Current top-down MS workflows have incorporated automated, on-line HPLC workflows to enable rapid desalting of nucleic acid samples for facile mass analysis without complication from adduction. Furthermore, optimization of MS/MS parameters utilizing collision, electron, or photon-based activation methods have enabled effective bond cleavage throughout the phosphodiester backbone while limiting secondary fragmentation, allowing characterization of progressively larger (~100 nt) nucleic acids and localization of covalent modifications. Development of software applications to perform automated identification of fragment ions has accelerated the broader adoption of mass spectrometry for analysis of nucleic acids. This review focuses on progress in tandem mass spectrometry for characterization of nucleic acids with particular emphasis on the software tools that have proven critical for advancing the field.

Chemical signaling is crucial during the insect lifespan, significantly affecting their survival, reproduction, and ecological interactions. Unfortunately, most chemical signals insects use are impossible for humans to perceive directly. Hence, mass spectrometry has become a vital tool by offering vital insight into the underlying chemical and biochemical processes in various variety of insect activities, such as communication, mate recognition, mating behavior, and adaptation (defense/attack mechanisms), among others. Here, we review different mass spectrometry-based strategies used to gain a deeper understanding of the chemicals involved in shaping the complex behaviors among insects and mass spectrometry-based research in insects that have direct impact in global economic activities.

Mass spectrometry (MS) is a powerful analytical technique that typically involves sample preparation and online analytical separation before MS detection. Traditional methods often face bottlenecks in sample preparation and analytical separation, despite the rapid detection capabilities of MS. This review explores the integration of electrokinetic manipulations directly with the ionization step to enhance MS performance, focusing on methods that eliminate or simplify sample preparation and separation processes. Techniques such as paper spray, electrophoresis in nanoelectrospray ionization (nESI) emitters, induced nESI, counterflow gradient electrofocusing, and in-syringe electrokinetics are highlighted for their ability to combine extraction and ionization in a single step, significantly improving throughput. The review delves into the use of electric fields during sample preparation and separations for these methods, demonstrating the efficiency of electrophoretic methods in driving extractions, crude separations, desalting, and enhanced sensitivity. The integration of these methods directly with MS ionization aims to enhance the analytical capabilities of mass spectrometry, while reducing costs and increasing throughput relative to traditional approaches.

Single particle mass analysis methods allow the measurement and characterization of individual nanoparticles, viral particles, as well as biomolecules like protein aggregates and complexes. Several key benefits are associated with the ability to analyze individual particles rather than bulk samples, such as high sensitivity and low detection limits, and virtually unlimited dynamic range, as this figure of merit strictly depends on analysis time. However, data processing and interpretation of single particle data can be complex, often requiring advanced algorithms and machine learning approaches. In addition, particle ionization, transfer, and detection efficiency can be limiting factors for certain types of analytes. Ongoing developments in the field aim to address these challenges and expand the capabilities of single particle mass analysis techniques. Charge detection mass spectrometry is a single particle version of mass spectrometry in which the charge (z) is determine independently from m/z. Nano-electromechanical resonator mass analysis relies on changes in a nanoscale device's resonance frequency upon deposition of a particle to directly derive its inertial mass. Mass photometry uses interferometric video-microscopy to derive particle mass from the intensity of the scattered light. A common feature of these approaches is the acquisition of single particle data, which can be filtered and concatenated in the form of a particle mass distribution. In the present article, dedicated to our honored colleague Richard Cole, we cover the latest technological advances and applications of these single particle mass analysis approaches.

A large part of the Human chemical exposome is now well characterized, and its health effects has been widely documented, although precise causal links remain difficult to establish. In parallel, genetic factors only were shown to contribute less than 30% to various pathologies. Therefore, environmental factors may represent the predominant cause of chronic diseases. Mass Spectrometry has been established for many years as a main "gold standard" in this field due to its performances both in sensitivity and selectivity. However, some unstable or highly reactive compounds may escape their detection in the biological samples because of their short half-life although some of their stable metabolites, if any, can be used for the exposure assessment. These electrophilic molecules are known to bind covalently to nucleophilic molecules in the body to form what are commonly called adducts. The study of adducts formed with DNA, proteins or with glutathione, nowadays called adductomics, can provide additional toxicologically relevant information in biomonitoring studies. This review describes this particular part of the reactive exposome and the related mass spectrometric methods developed therein. Three dedicated parts of this review are devoted to the contribution of mass spectrometry respectively to the assessment of DNA modifications, protein modifications, and reaction with glutathione.

Protein tandem mass spectrometry data are most often interpreted by matching observed mass spectra to a protein database derived from the reference genome of the sample being analyzed. In many application domains, however, a relevant protein database is unavailable or incomplete, and in such settings de novo sequencing is required. Since the introduction of the DeepNovo algorithm in 2017, the field of de novo sequencing has been dominated by deep learning methods, which use large amounts of labeled mass spectrometry data to train multi-layer neural networks to translate from observed mass spectra to corresponding peptide sequences. Here, we describe these deep learning methods, outline procedures for evaluating their performance, and discuss the challenges in the field, both in terms of methods development and evaluation protocols.

One of the great triumphs of mass spectrometry-based peptide and protein characterization is the characterization of their modifications as most modifications have a characteristic mass shift. What happens when the modification does not change the mass of the peptide? Here, the characterization of several peptide and proteins modifications that do not involve a mass shift are highlighted. Protein and peptide synthesis on ribosomes involves L-amino acids; however, posttranslational modifications (PTMs) can convert these L-amino acids into their D-isomers. As another example, nonenzymatic PTM of aspartate leads to the formation of three different isomers, with isoaspartate being the most prevalent. Both modifications do not alter the mass of the peptide and yet can have profound impact on the physicochemical characteristics of the peptide. Several MS and ion mobility techniques are highlighted, as are other methods such as chromatography, enzymatic enrichment, and labeling. The challenges inherent to these analytical methods and prospective developments in bioinformatics and computational strategies are discussed for these zero-dalton PTMs.