Mass Spectrometry-based Proteomic Techniques Research Articles

Integrating the analysis of human biopsies using post-translational modifications proteomics.

Proteome diversities and their biological functions are significantly amplified by post-translational modifications (PTMs) of proteins. Shotgun proteomics, which does not typically survey PTMs, provides an incomplete picture of the complexity of human biopsies in health and disease. Recent advances in mass spectrometry-based proteomic techniques that enrich and study PTMs are helping to uncover molecular detail from the cellular level to system-wide functions, including how the microbiome impacts human diseases. Protein heterogeneity and disease complexity are challenging factors that make it difficult to characterize and treat disease. The search for clinical biomarkers to characterize disease mechanisms and complexity related to patient diagnoses and treatment has proven challenging. Knowledge of PTMs is fundamentally lacking. Characterization of complex human samples that clarify the role of PTMs and the microbiome in human diseases will result in new discoveries. This review highlights the key role of proteomic techniques used to characterize unknown biological functions of PTMs derived from complex human biopsies. Through the integration of diverse methods used to profile PTMs, this review explores the genetic regulation of proteoforms, cells of origin expressing specific proteins, and several bioactive PTMs and their subsequent analyses by liquid chromatography and tandem mass spectrometry.

Cyanobacterial Proteomics: Diversity and Dynamics.

Cyanobacteria (oxygenic photoautrophs) comprise a diverse group holding significance both environmentally and for biotechnological applications. The utilization of proteomic techniques has significantly influenced investigations concerning cyanobacteria. Application of proteomics allows for large-scale analysis of protein expression and function within cyanobacterial systems. The cyanobacterial proteome exhibits tremendous functional, spatial, and temporal diversity regulated by multiple factors that continuously modify protein abundance, post-translational modifications, interactions, localization, and activity to meet the dynamic needs of these tiny blue greens. Modern mass spectrometry-based proteomics techniques enable system-wide examination of proteome complexity through global identification and high-throughput quantification of proteins. These powerful approaches have revolutionized our understanding of proteome dynamics and promise to provide novel insights into integrated cellular behavior at an unprecedented scale. In this Review, we present modern methods and cutting-edge technologies employed for unraveling the spatiotemporal diversity and dynamics of cyanobacterial proteomics with a specific focus on the methods used to analyze post-translational modifications (PTMs) and examples of dynamic changes in the cyanobacterial proteome investigated by proteomic approaches.

Insights into the time-course cellular effects triggered by iron oxide nanoparticles by combining proteomics with the traditional pharmacology strategy.

In recent years, a number of initially approved magnetic iron oxide nanoparticle (IONP)-based nano-medicines have been withdrawn due to the obscure nano-bio effects. Therefore, there is an urgent need to study the cellular effects triggered by IONPs on cells. In this study, we investigate the time-course cellular effects on the response of RAW 264.7 cells caused by Si-IONPs via pharmacological and mass spectrometry-based proteomics techniques. Our results revealed that Si-IONPs were internalized by clathrin-mediated endocytosis within 1 hour, and gradually degraded in endolysosomes over time, which might influence autophagy, oxidative stress, innate immune response, and inflammatory response after 12 hours. Our research provides a necessary assessment of Si-IONPs for further clinical treatment.

Isolation of Extracellular Vesicles Using Titanium Dioxide Microspheres.

Extracellular vesicles (EVs) are bilayer membrane particles released from several cell types to the extracellular environment. EVs have a crucial role in cell-cell communication, involving different biological processes in health and diseases. Due to the potential of biomarkers for several diseases as diagnostic and therapeutic tools, it is relevant to understand the biology of the EVs and their content. One of the current challenges involving EVs is regarding the purification method, which is a critical step for EV's functional and characterization studies. Ultracentrifugation is the most used method for EV isolation, where the nanoparticles are separated in sequential centrifugation to isolate the EVs based on their size. However, for viscous biofluids such as plasma, there is a co-isolation of the most abundant proteins, which can impair the EV's protein identification due to the low abundance of these proteins and signal suppression by the most abundant plasma proteins. Emerging techniques have gained attention in recent years. Titanium dioxide (TiO2) is one of the most promising techniques due to its property for selective isolation based on the interaction with phospholipids in the EV membrane. Using a small amount of TiO2 beads and a low volume of plasma, it is possible to isolate EVs with reduced plasma protein co-isolation. This study describes a comprehensive workflow for the isolation and characterization of plasma extracellular vesicles (EVs) using mass spectrometry-based proteomics techniques. The aim of this chapter is describe the EV isolation using TiO2 beads enrichment and high-throughput mass spectrometry techniques to efficiently identify the protein composition of EVs in a fast and straightforward manner.

EtOH-LN cryoembedding workflow to minimize freezing artifact in frozen tissues: A pilot study in preparing tissues compatible with mass spectrometry-based spatial proteomics application

Coolant-assisted liquid nitrogen (LN) flash freezing of frozen tissues has been widely adopted to preserve tissue morphology for histopathological annotations in mass spectrometry-based spatial proteomics techniques. However, existing coolants pose health risks upon inhalation and are expensive. To overcome this challenge, we present our pilot study by introducing the EtOH-LN workflow, which demonstrates the feasibility of using 95 % ethanol as a safer and easily accessible alternative to existing coolants for LN-based cryoembedding of frozen tissues. Our study reveals that both the EtOH-LN and LN-only cryoembedding workflows exhibit significantly reduced freezing artifacts compared to cryoembedding in cryostat (p < 0.005), while EtOH-LN (SD = 0.56) generates more consistent results compared to LN-only (SD = 1.29). We have modified a previously reported morphology restoration method to incorporate the EtOH-LN workflow, which successfully restored the tissue architecture from freezing artifacts (p < 0.05). Additional studies are required to validate the impact of the EtOH-LN workflow on the molecular profiles of tissues.

Potential biomarkers in peripheral blood mononuclear cells of patients with sporadic Ménière’s disease based on proteomics

Background Ménière’s disease (MD) mainly refers to the endolymphatic hydrops in membranous labyrinth of the inner ear. Application of the mass spectrometry-based proteomics techniques has not been applied in the field of MD. Objectives To search for potential differential proteins to identify the disease biomarkers and reveal disease bioinformatics-related mechanisms through applying protein technology to analyze the expression changes of peripheral blood mononuclear cells (PBMCs) in sporadic MD patients. Material and Methods 15 MD patients and 15 healthy individuals were enrolled. PBMCs from them were extracted, and their protein expression was identified and compared by LC-MS/MS and spectra analysis. Results There was significant difference in protein expression between MD patients and the control group. GO and KEGG analysis showed that endocytosis was involved in MD patients. Western blot results of CHMP1A and MMP9 protein showed that the expression of CHMP1A was higher in the MD group than that in the control group, while MMP9 was down-regulated. Immunohistochemistry confirmed that CHMP1A and MMP9 were expressed in the endolymphatic sacs of MD patients and in the inner ear of adult mice. Conclusions and Significance Endocytosis may be involved in the pathogenesis of sporadic MD, furthermore CHMP1A, VPS4A, FCN3 and MMP9 could be considered as potential biomarkers.

Serum proteome of dogs with chronic enteropathy.

Chronic enteropathy (CE) is common in dogs and can occur with multiple etiologies including food-responsive enteropathy (FRE) and idiopathic inflammatory bowel disease (IBD). To study the protein profile and pathway differences among dogs with FRE, IBD, and healthy controls using serum proteome analysis. Nine CE dogs with signs of gastrointestinal disease and histologically confirmed chronic inflammatory enteropathy and 16 healthy controls. A cross-sectional study with cases recruited from 2 veterinary hospitals between May 2019 and November 2020 was performed. Serum samples were analyzed using mass spectrometry-based proteomic techniques. Proteomic profiles showed marked variation in relative protein abundances. Forty-five proteins were significantly (P ≤ .01) differentially expressed among the dogs with CE and controls with ≥2-fold change in abundance. The fold change of dogs with IBD normalized to controls was more pronounced for the majority of proteins than that seen in the dogs with FRE normalized to control dogs. Proteins involving reactive oxygen species, cytokine activation, acute phase response signaling, and lipid metabolism were altered in dogs with CE. Cytokine alterations, acute phase response signaling, and lipid metabolism are likely involved in pathogenesis of CE. Although there are insufficient current data to justify the use of proteomic biomarkers for assessment of CE in dogs, our study identifies potential candidates.

Proteomic analysis of protein lysine 2-hydroxyisobutyrylation (Khib) in soybean leaves

BackgroundProtein lysine 2-hydroxyisobutyrylation (Khib) is a novel post-translational modification (PTM) discovered in cells or tissues of animals, microorganisms and plants in recent years. Proteome-wide identification of Khib-modified proteins has been performed in several plant species, suggesting that Khib-modified proteins are involved in a variety of biological processes and metabolic pathways. However, the protein Khib modification in soybean, a globally important legume crop that provides the rich source of plant protein and oil, remains unclear.ResultsIn this study, the Khib-modified proteins in soybean leaves were identified for the first time using affinity enrichment and high-resolution mass spectrometry-based proteomic techniques, and a systematic bioinformatics analysis of these Khib-modified proteins was performed. Our results showed that a total of 4251 Khib sites in 1532 proteins were identified as overlapping in three replicates (the raw mass spectrometry data are available via ProteomeXchange with the identifier of PXD03650). These Khib-modified proteins are involved in a wide range of cellular processes, particularly enriched in biosynthesis, central carbon metabolism and photosynthesis, and are widely distributed in subcellular locations, mainly in chloroplasts, cytoplasm and nucleus. In addition, a total of 12 sequence motifs were extracted from all identified Khib peptides, and a basic amino acid residue (K), an acidic amino acid residue (E) and three aliphatic amino acid residues with small side chains (G/A/V) were found to be more preferred around the Khib site. Furthermore, 16 highly-connected clusters of Khib proteins were retrieved from the global PPI network, which suggest that Khib modifications tend to occur in proteins associated with specific functional clusters.ConclusionsThese findings suggest that Khib modification is an abundant and conserved PTM in soybean and that this modification may play an important role in regulating physiological processes in soybean leaves. The Khib proteomic data obtained in this study will help to further elucidate the regulatory mechanisms of Khib modification in soybean in the future.

Trends in deamidation across archaeological bones, ceramics and dental calculus.

The accumulation of post-translational modifications (PTMs) in proteins throughout the lifecycle has been studied for decades, particularly more so with the advent of soft-ionization mass spectrometry-based proteomic techniques. However, particular PTMs, such as the deamidations of asparagine and glutamine residues, continue to accumulate in proteins that remain into the forensic, archaeological, and palaeontological records. The accurate measurement of these ancient 'molecular timers' has been proposed as a method to not only differentiate between exogenous and endogenous proteins within complex mixtures (i.e., contamination), but also as a method of providing relative age estimations into geological time. In this study we explored the extent to which deamidation varies with chronological age across different proteins in bones, as well as investigated differences between proteins across dental calculus and archaeological ceramics. We also analysed the relationships between the observed extent of deamidation and the protein primary structure. We found that collagen obtained from archaeological bones showed a chronological dependence on the extent of deamidation observed, but only when they were from similar environments, supporting prior suggestions about 'thermal age' being a major influence on the deamidation observed. Our study on non-collagenous proteins (NCPs) in archaeological bones showed that while biglycan, and to a lesser extent chondroadherin, showed positive correlations between geological age and the extent of deamidation, others including fetuin-A and serum albumin did not. However, despite the well-known dependence of deamidation on the three-dimensional structure of the peptides, we were unable to find any clear correlation between the structural motifs of the peptides in archaeological bones and the extent of deamidation observed. Our analysis of a set of food proteins obtained from Neolithic archaeological ceramics in Çatalhöyük also showed similar deamidation levels irrespective of the protein structure. Overall, our results suggest that deamidation in archaeological samples could be useful for obtaining additional information beyond identification of species and tissue type, be that as a measure of protein endogeneity and potential contamination, or a measure of protein degradation, or as an indicator of thermal age and for relative dating; however, further research needs to be undertaken to understand why particular proteins are better for this than others, going beyond simple consideration of their secondary structure.

Molecular Proteomics and Signalling of Human Platelets in Health and Disease

Platelets are small anucleate blood cells that play vital roles in haemostasis and thrombosis, besides other physiological and pathophysiological processes. These roles are tightly regulated by a complex network of signalling pathways. Mass spectrometry-based proteomic techniques are contributing not only to the identification and quantification of new platelet proteins, but also reveal post-translational modifications of these molecules, such as acetylation, glycosylation and phosphorylation. Moreover, target proteomic analysis of platelets can provide molecular biomarkers for genetic aberrations with established or non-established links to platelet dysfunctions. In this report, we review 67 reports regarding platelet proteomic analysis and signalling on a molecular base. Collectively, these provide detailed insight into the: (i) technical developments and limitations of the assessment of platelet (sub)proteomes; (ii) molecular protein changes upon ageing of platelets; (iii) complexity of platelet signalling pathways and functions in response to collagen, rhodocytin, thrombin, thromboxane A2 and ADP; (iv) proteomic effects of endothelial-derived mediators such as prostacyclin and the anti-platelet drug aspirin; and (v) molecular protein changes in platelets from patients with congenital disorders or cardiovascular disease. However, sample sizes are still low and the roles of differentially expressed proteins are often unknown. Based on the practical and technical possibilities and limitations, we provide a perspective for further improvements of the platelet proteomic field.

Proteomic analysis of ubiquitination substrates reveals a CTLH E3 ligase complex-dependent regulation of glycolysis.

Ubiquitination is an essential post‐translational modification that regulates protein stability or function. Its substrate specificity is dictated by various E3 ligases. The human C‐terminal to LisH (CTLH) complex is a newly discovered multi‐subunit really interesting new gene (RING) E3 ligase with only a few known ubiquitination targets. Here, we used mass spectrometry‐based proteomic techniques to gain insight into CTLH complex function and ubiquitination substrates in HeLa cells. First, global proteomics determined proteins that were significantly increased, and thus may be substrates targeted for degradation, in cells depleted of CTLH complex member RanBPM. RanBPM‐dependent ubiquitination determined using diGLY‐enriched proteomics and the endogenous RanBPM interactome further revealed candidate ubiquitination targets. Three glycolysis enzymes alpha‐enolase, L‐lactate dehydrogenase A chain (LDHA), and pyruvate kinase M1/2 (PKM) had decreased ubiquitin sites in shRanBPM cells and were found associated with RanBPM in the interactome. Reduced polyubiquitination was validated for PKM2 and LDHA in cells depleted of RanBPM and CTLH complex RING domain subunit RMND5A. PKM2 and LDHA protein levels were unchanged, yet their activity was increased in extracts of cells with downregulated RanBPM. Finally, RanBPM deficient cells displayed enhanced glycolysis and deregulated central carbon metabolism. Overall, this study identifies potential CTLH complex ubiquitination substrates and uncovers that the CTLH complex inhibits glycolysis via non‐degradative ubiquitination of PKM2 and LDHA.

Advances in quantitative high-throughput phosphoproteomics with sample multiplexing.

Eukaryotic protein phosphorylation modulates nearly every major biological process. Phosphorylation regulates protein activity, mediates cellular signal transduction, and manipulates cellular structure. Consequently, the dysregulation of kinase and phosphatase pathways has been linked to a multitude of diseases. Mass spectrometry-based proteomic techniques are increasingly used for the global interrogation of perturbations in phosphorylation-based cellular signaling. Strategies for studying phosphoproteomes require high-specificity enrichment, sensitive detection, and accurate localization of phosphorylation sites with advanced LC-MS/MS techniques and downstream informatics. Sample multiplexing with isobaric tags has also been integral to recent advancements in throughput and sensitivity for phosphoproteomic studies. Each of these facets of phosphoproteomics analysis present distinct challenges and thus opportunities for improvement and innovation. Here, we review current methodologies, explore persistent challenges, and discuss the outlook for isobaric tag-based quantitative phosphoproteomic analysis.

Thermal proteome profiling efficiently identifies ribosome destabilizing oxazolidinones

Identifying the targets of bioactive small molecules is a challenging endeavor for which no general solution currently exists. Classical affinity purification experiments suffer from the need to functionalise a bioactive compound and link it to a solid support, which may interfere with target binding. A modern mass spectrometry-based proteomics technique that has partially circumvented this problem is thermal proteome profiling (TPP), which determines the effect of an unmodified small molecule on the thermal stability of the whole proteome simultaneously. Here, we use TPP to identify the mode-of-action of a newly-discovered autophagy inhibitor based on oxazolidinones often employed as chiral auxiliaries. Surprisingly, a significant portion of all ribosomal proteins were found to be destabilized by the inhibitor, highlighting the utility of this technology for determining a challenging mode-of-action.

Recent advances in proteome-wide label-free target deconvolution for bioactive small molecules.

Small-molecule drugs modulate biological processes and disease states through engagement of target proteins in cells. Assessing drug-target engagement on a proteome-wide scale is of utmost importance in better understanding the molecular mechanisms of action of observed beneficial and adverse effects, as well as in developing next generation tool compounds and drugs with better efficacies and specificities. However, systematic assessment of drug-target engagement has been an arduous task. With the continuous development of mass spectrometry-based proteomics instruments and techniques, various chemical proteomics approaches for drug target deconvolution (i.e., the identification of molecular target for drugs) have emerged. Among these, the label-free target deconvolution approaches that do not involve the chemical modification of compounds of interest, have gained increased attention in the community. Here we provide an overview of the basic principles and recent biological applications of the most important label-free methods including the cellular thermal shift assay, pulse proteolysis, chemical denaturant and protein precipitation, stability of proteins from rates of oxidation, drug affinity responsive target stability, limited proteolysis, and solvent-induced protein precipitation. The state-of-the-art technical implications and future outlook for the label-free approaches are also discussed.

Collagen 24 α1 Is Increased in Insulin-Resistant Skeletal Muscle and Adipose Tissue.

Aberrant extracellular matrix (ECM) remodelling in muscle, liver and adipose tissue is a key characteristic of obesity and insulin resistance. Despite its emerging importance, the effective ECM targets remain largely undefined due to limitations of current approaches. Here, we developed a novel ECM-specific mass spectrometry-based proteomics technique to characterise the global view of the ECM changes in the skeletal muscle and liver of mice after high fat (HF) diet feeding. We identified distinct signatures of HF-induced protein changes between skeletal muscle and liver where the ECM remodelling was more prominent in the muscle than liver. In particular, most muscle collagen isoforms were increased by HF diet feeding whereas the liver collagens were differentially but moderately affected highlighting a different role of the ECM remodelling in different tissues of obesity. Moreover, we identified a novel association between collagen 24α1 and insulin resistance in the skeletal muscle. Using quantitative gene expression analysis, we extended this association to the white adipose tissue. Importantly, collagen 24α1 mRNA was increased in the visceral adipose tissue, but not the subcutaneous adipose tissue of obese diabetic subjects compared to lean controls, implying a potential pathogenic role of collagen 24α1 in obesity and type 2 diabetes.

Nanoparticles: Synthesis, Morphophysiological Effects, and Proteomic Responses of Crop Plants.

Plant cells are frequently challenged with a wide range of adverse environmental conditions that restrict plant growth and limit the productivity of agricultural crops. Rapid development of nanotechnology and unsystematic discharge of metal containing nanoparticles (NPs) into the environment pose a serious threat to the ecological receptors including plants. Engineered nanoparticles are synthesized by physical, chemical, biological, or hybrid methods. In addition, volcanic eruption, mechanical grinding of earthquake-generating faults in Earth’s crust, ocean spray, and ultrafine cosmic dust are the natural source of NPs in the atmosphere. Untying the nature of plant interactions with NPs is fundamental for assessing their uptake and distribution, as well as evaluating phytotoxicity. Modern mass spectrometry-based proteomic techniques allow precise identification of low abundant proteins, protein–protein interactions, and in-depth analyses of cellular signaling networks. The present review highlights current understanding of plant responses to NPs exploiting high-throughput proteomics techniques. Synthesis of NPs, their morphophysiological effects on crops, and applications of proteomic techniques, are discussed in details to comprehend the underlying mechanism of NPs stress acclimation.

Analysis of apoplastic proteins expressed during net form net blotch of barley

The net form net blotch (NFNB) is a significant disease of barley. Its causal agent, Pyrenophora teres f. teres (PTT), has an important economic impact on yield and grain quality globally. However, the molecular interaction between PTT and barley is not fully understood. The plant–pathogen encounter comprises the secretion of diverse molecules involved in plant defence, including pathogenicity-related proteins, and fungal attack, such as proteinaceous toxins called effectors. The forefront of the molecular crosstalk between plant and fungus is the space between plant cells or apoplast. To explore the suitability of studying apoplastic proteins to assist understanding the host–pathogen interaction, a mass spectrometry-based proteomics technique was used to profile apoplastic protein differences in control and NFNB-infected leaves in a susceptible cultivar. The analysis revealed 1130 barley proteins, of which 140 were found to be significantly differentially expressed. This paper presents an overview of the major protein changes induced in the barley apoplast and discusses the involvement of individual proteins in defence and disease development. Our results suggest that the fungus may be hijacking defence signalling pathways. This investigation provides the first in vivo proteomics data for a NFNB–barley interaction, setting a background for further studies.

A Proteomic Atlas of Cardiac Amyloidosis

The transthyretin (TTR) and immunoglobulin light chain proteins do not exist in isolation in cardiac amyloid (CA) plaques. Laser microdissection followed by mass spectrometry-based proteomic (LMD-MS) typing techniques can identify hundreds of co-deposited proteins in the "nano-environment" of amyloid deposits. Some, such as the "amyloid signature" proteins (SAP, APOE, APOA4, vitronectin, clusterin), are specific for amyloid plaques across different tissues and amyloid types. However, many of the remaining proteins are also abundant in the serum or normal tissues making it difficult to discern if they are unique to the amyloid plaque or part of the normal tissue background. We included 288 patients/samples with TTR CA (of which 53 were mutated) diagnosed by endomyocardial biopsy and 5 normal control samples obtained from 3 patients during autopsy. At the time of the meeting updated analyses including 168 cardiac light chain amyloid patients and 15 controls from patients with restrictive and hypertensive cardiomyopathy will be presented. Normalized spectral counts were used as a semi-quantitative measure of abundance. Proteins were considered part of the proteome if their abundance in the amyloid plaque was increased by 1.5-fold compared to normal controls (FDR p&lt;0.05). Of 2240 unique proteins identified across all samples, 42 were differentially expressed in amyloid plaques. These included a) signature proteins: SAP, APOE, APOA4, vitronectin, clusterin; b) serum proteins: albumin, b2-glycoprotein, 7 complement pathway proteins; c) matrix proteins: 2 collagen isoforms, fibulin 1, decorin, PCOLCE2, TIMP3; d) cytosketal and contractile proteins: 2 actin isoforms, MYL2, 8 myosin isoforms, 3 ankyrin isofroms, desmin; and "other" proteins: serpine2, MAGE-like protein-2, pleiotrophin, AMBP, SRPX and QSOX1). The signature and cytoskeletal proteins were the most abundant overall, however, proteins that were most increased compared to normal included (log2 fold change in parentheses): fibulin (24.5), PCOLCE2 (23.5), b2-glycoprotein (23.5), factor H related peptide-2 (24.2), serpine2 (24.7), mage-like protein-2 (22.8), pleiotrophin (23.8), QSOX1 (22.9), SRPX (23.5). B2 glycoprotein was more abundant in wild type TTR samples(p=0.003). APOE (p=0.002), fibulin (p=0.008) and serpine2 (p&lt;0.0001) were more abundant in UK stage (Gilmore JD et al, Eur Heart J 2018) 2/3 patients. Unsupervised hierarchical clustering of patients by normalized protein abundance revealed two major distinct patterns of co-deposited proteins (figure). Patients with high levels of contractility proteins (myosin isoforms, desmin, actins) were characterized by low levels of most other proteins (clusters on the left). Most complement proteins co-deposited along with higher levels of signature proteins (clusters on the right). When comparing clinical and laboratory characteristics between those 2 groups of patients only cardiac strain was found to be significantly higher (worse) in patients with lower levels of contractility proteins (p=0.01). Our data shows that the TTR CA proteome includes signature, serum and cardiac tissue proteins with variable expression according to TTR mutation status and cardiac functional status, which could inform mechanisms of disease pathogenesis. Comparison with diseased controls may further clarify if this proteomic pattern is specific to CA. Figure Disclosures Dasari: The Binding Site: Patents &amp; Royalties: US Patent Rights on Mass Spectroscopy Licensing agreement with The Binding Site, Research Funding. Dispenzieri:Akcea: Consultancy; Intellia: Consultancy; Janssen: Consultancy; Pfizer: Research Funding; Takeda: Research Funding; Celgene: Research Funding; Alnylam: Research Funding.

The epigenetics of diabetes, obesity, overweight and cardiovascular disease.

The objectives of this review were once to understand the roles of the epigenetics mechanism in different types of diabetes, obesity, overweight, and cardiovascular disease. Epigenetics represents a phenomenon of change heritable phenotypic expression of genetic records taking place except changes in DNA sequence. Epigenetic modifications can have an impact on a whole of metabolic disease with the aid of specific alteration of candidate genes based totally on the change of the target genes. In this review, I summarized the new findings in DNA methylation, histone modifications in each type of diabetes (type 1 and type 2), obesity, overweight, and cardiovascular disease. The involvement of histone alterations and DNA methylation in the development of metabolic diseases is now widely accepted recently many novel genes have been demonstrated that has roles in diabetes pathway and it can be used for detection prediabetic; however Over the modern-day years, mass spectrometry-based proteomics techniques positioned and mapped one-of a kind range of histone modifications linking obesity and metabolic diseases. The main point of these changes is rapidly growing; however, their points and roles in obesity are no longer properly understood in obesity. Furthermore, epigenetic seen in cardiovascular treatment revealed a massive quantity of modifications affecting the improvement and development of cardiovascular disease. In addition, epigenetics are moreover involved in cardiovascular risk factors such as smoking. The aberrant epigenetic mechanisms that make a contribution to cardiovascular disease.

Mass spectrometry-based proteomic techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections. A systematic review

Central nervous system (CNS) infections account for considerable death and disability every year. An urgent research priority is scaling up diagnostic capacity, and introduction of point-of-care tests. We set out to assess current evidence for the application of mass spectrometry (MS) peptide sequencing in identification of diagnostic biomarkers for CNS infections. We performed a systematic review (PROSPEROCRD42018104257) using PRISMA guidelines on use of MS to identify cerebrospinal fluid (CSF) biomarkers for diagnosing CNS infections. We searched PubMed, Embase, Web of Science, and Cochrane for articles published from 1 January 2000 to 1 February 2019, and contacted experts. Inclusion criteria involved primary research except case reports, on the diagnosis of infectious diseases except HIV, applying MS to human CSF samples, and English language. 4,620 papers were identified, of which 11 were included, largely confined to pre-clinical biomarker discovery, and eight (73%) published in the last five years. 6 studies performed further work termed verification or validation. In 2 of these studies, it was possible to extract data on sensitivity and specificity of the biomarkers detected by ELISA, ranging from 89-94% and 58-92% respectively. The findings demonstrate feasibility and potential of the methods in a variety of infectious diseases, but emphasise the need for strong interdisciplinary collaborations to ensure appropriate study design and biomarker validation.