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1.
Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products.
Moyer, TB, Parsley, NC, Sadecki, PW, Schug, WJ, Hicks, LM
Natural product reports. 2021;(3):489-509
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Abstract
Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.
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Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence.
Man, L, Klare, WP, Dale, AL, Cain, JA, Cordwell, SJ
Biochemical Society transactions. 2021;(5):1905-1926
Abstract
Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.
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Critical role of mass spectrometry proteomics in tear biomarker discovery for multifactorial ocular diseases (Review).
Ma, JYW, Sze, YH, Bian, JF, Lam, TC
International journal of molecular medicine. 2021;(5)
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Abstract
The tear film is a layer of body fluid that maintains the homeostasis of the ocular surface. The superior accessibility of tears and the presence of a high concentration of functional proteins make tears a potential medium for the discovery of non‑invasive biomarkers in ocular diseases. Recent advances in mass spectrometry (MS) have enabled determination of an in‑depth proteome profile, improved sensitivity, faster acquisition speed, proven variety of acquisition methods, and identification of disease biomarkers previously lacking in the field of ophthalmology. The use of MS allows efficient discovery of tear proteins, generation of reproducible results, and, more importantly, determines changes of protein quantity and post‑translation modifications in microliter samples. The present review compared techniques for tear collection, sample preparation, and acquisition applied for the discovery of tear protein markers in normal subjects and multifactorial conditions, including dry eye syndrome, diabetic retinopathy, thyroid eye disease and primary open‑angle glaucoma, which require an early diagnosis for treatment. It also summarized the contribution of MS to early discovery by means of disease‑related protein markers in tear fluid and the potential for transformation of the tear MS‑based proteome to antibody‑based assay for future clinical application.
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Proteoform characterization based on top-down mass spectrometry.
Zhong, J, Sun, Y, Xie, M, Peng, W, Zhang, C, Wu, FX, Wang, J
Briefings in bioinformatics. 2021;(2):1729-1750
Abstract
Proteins are dominant executors of living processes. Compared to genetic variations, changes in the molecular structure and state of a protein (i.e. proteoforms) are more directly related to pathological changes in diseases. Characterizing proteoforms involves identifying and locating primary structure alterations (PSAs) in proteoforms, which is of practical importance for the advancement of the medical profession. With the development of mass spectrometry (MS) technology, the characterization of proteoforms based on top-down MS technology has become possible. This type of method is relatively new and faces many challenges. Since the proteoform identification is the most important process in characterizing proteoforms, we comprehensively review the existing proteoform identification methods in this study. Before identifying proteoforms, the spectra need to be preprocessed, and protein sequence databases can be filtered to speed up the identification. Therefore, we also summarize some popular deconvolution algorithms, various filtering algorithms for improving the proteoform identification performance and various scoring methods for localizing proteoforms. Moreover, commonly used methods were evaluated and compared in this review. We believe our review could help researchers better understand the current state of the development in this field and design new efficient algorithms for the proteoform characterization.
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Mass Spectrometry for Analysis of Changes during Food Storage and Processing.
Cao, G, Li, K, Guo, J, Lu, M, Hong, Y, Cai, Z
Journal of agricultural and food chemistry. 2020;(26):6956-6966
Abstract
Many physicochemical changes occur during food storage and processing, such as rancidity, hydrolysis, oxidation, and aging, which may alter the taste, flavor, and texture of food products and pose risks to public health. Analysis of these changes has become of great interest to many researchers. Mass spectrometry is a promising technique for the study of food and nutrition domains as a result of its excellent ability in molecular profiling, food authentication, and marker detection. In this review, we summarized recent advances in mass spectrometry techniques and their applications in food storage and processing. Furthermore, current technical challenges associated with these methodologies were discussed.
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Calibration strategies for elemental analysis of biological samples by LA-ICP-MS and LIBS - A review.
Martinez, M, Baudelet, M
Analytical and bioanalytical chemistry. 2020;(1):27-36
Abstract
Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and laser-induced breakdown spectroscopy (LIBS) are widely accepted techniques for direct sampling of biological materials for elemental analysis, with increasing applications being reported over the recent years. This review is focused on the calibration materials used to quantify trace elements in different biological samples such as soft tissues (for instance brain, liver, hair) and hard tissues (bones and teeth). The design of a correct calibration strategy relies on the choice of an adapted reference material that can be commercially available or prepared in-house, which will be reviewed here. A large variety of methods has been approached and considered promising over the years, and the development of matrix-matched reference biological materials seems now closer than ever and gives hope to even better quantitation using LIBS and LA-ICP-MS.
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Mass spectrometry-based lipidomics in food science and nutritional health: A comprehensive review.
Sun, T, Wang, X, Cong, P, Xu, J, Xue, C
Comprehensive reviews in food science and food safety. 2020;(5):2530-2558
Abstract
With the advance in science and technology as well as the improvement of living standards, the function of food is no longer just to meet the needs of survival. Food science and its associated nutritional health issues have been increasingly debated. Lipids, as complex metabolites, play a key role both in food and human health. Taking advantages of mass spectrometry (MS) by combining its high sensitivity and accuracy with extensive selective determination of all lipid classes, MS-based lipidomics has been employed to resolve the conundrum of addressing both qualitative and quantitative aspects of high-abundance and low-abundance lipids in complex food matrices. In this review, we systematically summarize current applications of MS-based lipidomics in food field. First, common MS-based lipidomics procedures are described. Second, the applications of MS-based lipidomics in food science, including lipid composition characterization, adulteration, traceability, and other issues, are discussed. Third, the application of MS-based lipidomics for nutritional health covering the influence of food on health and disease is introduced. Finally, future research trends and challenges are proposed. MS-based lipidomics plays an important role in the field of food science, promoting continuous development of food science and integration of food knowledge with other disciplines. New methods of MS-based lipidomics have been developed to improve accuracy and sensitivity of lipid analysis in food samples. These developments offer the possibility to fully characterize lipids in food samples, identify novel functional lipids, and better understand the role of food in promoting healt.
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MASS SPECTROMETRY-BASED MITOCHONDRIAL PROTEOMICS IN HUMAN OVARIAN CANCERS.
Li, N, Zhan, X
Mass spectrometry reviews. 2020;(5-6):471-498
Abstract
The prominent characteristics of mitochondria are highly dynamic and regulatory, which have crucial roles in cell metabolism, biosynthetic, senescence, apoptosis, and signaling pathways. Mitochondrial dysfunction might lead to multiple serious diseases, including cancer. Therefore, identification of mitochondrial proteins in cancer could provide a global view of tumorigenesis and progression. Mass spectrometry-based quantitative mitochondrial proteomics fulfils this task by enabling systems-wide, accurate, and quantitative analysis of mitochondrial protein abundance, and mitochondrial protein posttranslational modifications (PTMs). Multiple quantitative proteomics techniques, including isotope-coded affinity tag, stable isotope labeling with amino acids in cell culture, isobaric tags for relative and absolute quantification, tandem mass tags, and label-free quantification, in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides, increase flexibility for researchers to study mitochondrial proteomes. This article reviews isolation and purification of mitochondria, quantitative mitochondrial proteomics, quantitative mitochondrial phosphoproteomics, mitochondrial protein-involved signaling pathway networks, mitochondrial phosphoprotein-involved signaling pathway networks, integration of mitochondrial proteomic and phosphoproteomic data with whole tissue proteomic and transcriptomic data and clinical information in ovarian cancers (OC) to in-depth understand its molecular mechanisms, and discover effective mitochondrial biomarkers and therapeutic targets for predictive, preventive, and personalized treatment of OC. This proof-of-principle model about OC mitochondrial proteomics is easily implementable to other cancer types. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Using X-ray Footprinting and Mass Spectrometry to Study the Structure and Function of Membrane Proteins.
Gupta, S
Protein and peptide letters. 2019;(1):44-54
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Abstract
BACKGROUND Membrane proteins are crucial for cellular sensory cascades and metabolite transport, and hence are key pharmacological targets. Structural studies by traditional highresolution techniques are limited by the requirements for high purity and stability when handled in high concentration and nonnative buffers. Hence, there is a growing requirement for the use of alternate methods in a complementary but orthogonal approach to study the dynamic and functional aspects of membrane proteins in physiologically relevant conditions. In recent years, significant progress has been made in the field of X-ray radiolytic labeling in combination with mass spectroscopy, commonly known as X-ray Footprinting and Mass Spectrometry (XFMS), which provide residue-specific information on the solvent accessibility of proteins. In combination with both lowresolution biophysical methods and high-resolution structural data, XFMS is capable of providing valuable insights into structure and dynamics of membrane proteins, which have been difficult to obtain by standalone high-resolution structural techniques. The XFMS method has also demonstrated a unique capability for identification of structural waters and their dynamics in protein cavities at both a high degree of spatial and temporal resolution, and thus capable of identifying conformational hot-spots in transmembrane proteins. CONCLUSION We provide a perspective on the place of XFMS amongst other structural biology methods and showcase some of the latest developments in its usage for studying conformational changes in membrane proteins.
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Fast Photochemical Oxidation of Proteins Coupled with Mass Spectrometry.
Shi, L, Gross, ML
Protein and peptide letters. 2019;(1):27-34
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Abstract
BACKGROUND Determination of the composition and some structural features of macromolecules can be achieved by using structural proteomics approaches coupled with mass spectrometry (MS). One approach is hydroxyl radical protein footprinting whereby amino-acid side chains are modified with reactive reagents to modify irreversibly a protein side chain. The outcomes, when deciphered with mass-spectrometry-based proteomics, can increase our knowledge of structure, assembly, and conformational dynamics of macromolecules in solution. Generating the hydroxyl radicals by laser irradiation, Hambly and Gross developed the approach of Fast Photochemical Oxidation of Proteins (FPOP), which labels proteins on the sub millisecond time scale and provides, with MS analysis, deeper understanding of protein structure and protein-ligand and protein- protein interactions. This review highlights the fundamentals of FPOP and provides descriptions of hydroxyl-radical and other radical and carbene generation, of the hydroxyl labeling of proteins, and of determination of protein modification sites. We also summarize some recent applications of FPOP coupled with MS in protein footprinting. CONCLUSION We survey results that show the capability of FPOP for qualitatively measuring protein solvent accessibility on the residue level. To make these approaches more valuable, we describe recent method developments that increase FPOP's quantitative capacity and increase the spatial protein sequence coverage. To improve FPOP further, several new labeling reagents including carbenes and other radicals have been developed. These growing improvements will allow oxidative- footprinting methods coupled with MS to play an increasingly significant role in determining the structure and dynamics of macromolecules and their assemblies.