Mass Spectrometry Techniques: Principles and Practices for Quantitative Proteomics

Identification of unique biomarkers for proliferative diabetic retinopathy with tractional retinal detachment by proteomics profiling of vitreous humor

Diabetic retinopathy (DR) is one of the major complications of diabetes, resulting in severe vision loss. Traction retinal detachment (TRD) is the main factor affecting the effect of proliferative diabetic retinopathy (PDR) surgery. Liquid Chromatography with tandem mass spectrometry (LC-MS/MS) was adopted to analyze the proteomes of the vitreous in the TRD, vitreous hemorrhage (VH) and macular hole (MH) groups. By employing bioinformatics tools for GO and KEGG pathway annotation, as well as conducting protein-protein interaction(PPI) network analysis, we investigated the functional enrichment of proteins in the TRD vitreous and their associated pathways. Additionally, peptide center analysis was performed on the proteomic data to identify key differentially expressed proteins based on screening results. Bioinformatics analysis showed that DEPs is mainly enriched in the complement, the coagulation cascade systems and regulation of actin cytoskeleton. The protein interaction network analysis showed that the central proteins were mainly related to sphingolipid metabolism. APOA4, CHI3L1, LTBP2 were significantly up-regulated in TRD, which were related to the complement system, coagulation cascade and platelet activation, sphingolipid metabolism and other pathways. APOA4 and CHI3L1 protein in patients with TRD group raised significantly in the vitreous humor, shows the potential biomarkers for TRD.

Chemical composition analysis of the proteins of leech extract with anti-pulmonary fibrosis and their effects on metabolomics based on chromatography-mass spectrometry

Idiopathic pulmonary fibrosis is a high-mortality chronic lung disease, and currently existing medications have limited therapeutic efficacy with noticeable adverse effects, urgently necessitating the exploration of more effective and safer treatment options. Our preliminary studies have demonstrated that the leech extract group with molecular weight greater than 10 kDa (>10 kDa group) exhibited superior anti-idiopathic pulmonary fibrosis efficacy. To trace the active components of > 10 kDa group, it was separated by gel electrophoresis and analyzed by Nano LC-MS/MS. To further analyze the effects of these active components on the regulation of metabolic pathways in fibrotic lung tissue, the metabolites of lung tissue were analyzed by UPLC/MS after administration of > 10 kDa group in bleomycin-induced pulmonary fibrosis (BML-induced PF) mice for 28 days at a 0.179 mg/g per day. A total of 17 proteins were identified in > 10 kDa group and 46 endogenous metabolites were identified in lung tissue, among which 18 significantly differential metabolites were screened as potential metabolomics biomarkers. Metabolic pathway analysis demonstrated that these identified differential metabolites mainly involved biosynthesis of unsaturated fatty acids, phenylalanine-tyrosine and tryptophan biosynthesis and tryptophan metabolism signaling pathway, indicating that the active components of > 10 kDa group mainly regulated the metabolic disorders of lung tissue in BLM-induced mice by up-regulating the biosynthesis of unsaturated fatty acids, down-regulating phenylalanine-tyrosine and tryptophan biosynthesis, and adjusting tryptophan metabolism signaling pathway.

Salivary proteomics as signature for molar incisor hypomineralization stages

OBJECTIVE

Saliva is a rich-bodily fluid with recognized clinical diagnosis roles. This research aimed to investigate the salivary proteomic signatures for MIH in children with distinct degrees of severity.

MATERIALS AND METHODS

In this cross-sectional study, 50 schoolers (8-13 years) were equally assigned into the following groups: G1 (Control group-Healthy first permanent molars), G2 (Mild MIH with white/creamy opacity and free of caries), G3 (Mild MIH with yellow/brown opacity and free of caries), G4 (Severe MIH with white/creamy, yellow/brown opacities including post-eruptive fracture and free of caries), G5 (Severe MIH with white/creamy, yellow/brown opacities, post-eruptive fracture, and caries). Unstimulated saliva samples were collected and later explored using mass spectrometry analysis.

RESULTS

In total, 6,471 proteins were found, 5,073 exclusively from MIH children, and 778 overlapping among the different degrees of the disturb. The biological pathways displayed distinct patterns among the groups, which differed according to the MIH degrees. Gene-Ontology differences might not be verified regarding the biological processes and cellular components. Conversely, concerning molecular function, alterations among groups were evident, with proteins that would contribute to MIH in children with the severe condition (i.e., calcium ion binding, microtubule binding, platelet-derived growth factor binding).

CONCLUSION

The results of this study support important salivary proteomics changes in MIH children according to distinct degrees of severity, reinforcing the interplay between the clinical characteristics and changes in the salivary proteome.

CLINICAL RELEVANCE

Changes occurring in the salivary proteomics of children with distinct degrees of severity of Molar Incisor Hypomineralization (MIH) might be promising biomarkers and valuable information in clinical care, helping professionals make better clinical decisions and helping patients to understand their disturbance.

Venoms and Extracellular Vesicles: A New Frontier in Venom Biology

Extracellular vesicles (EVs) are nanoparticle-sized vesicles secreted by nearly all cell types under normal physiological conditions. In toxicological research, EVs have emerged as a crucial link between public health and multi-omics approaches, offering insights into cellular responses to disease-causing injury agents such as environmental and biological toxins, contaminants, and drugs. Notably, EVs present a unique opportunity to deepen our understanding of the pathophysiology of envenomation by natural toxins. Recent advancements in isolating and purifying EV cargo, mass spectrometry techniques, and bioinformatics have positioned EVs as potential biomarkers that could elucidate biological signaling pathways and provide valuable information on the relationship between venomous toxins, their mechanisms of action, and the effectiveness of antivenoms. Additionally, EVs hold promise as proxies for various aspects of envenomation, including the toxin dosage, biological characterization, injury progression, and prognosis during therapeutic interventions. These aspects can be explored through multi-omics technology applied to EV contents from the plasma, saliva, or urine samples of envenomated individuals, offering a comprehensive integrative approach to understanding and managing envenomation cases.

Assessing inorganic nanoparticle toxicity through omics approaches

In the last two decades, the development of nanotechnology has resulted in inorganic nanoparticles playing crucial roles in key industries, ranging from healthcare to energy technologies. For instance, gold and silver nanoparticles are widely used in rapid COVID-19 and flu tests, titania and zinc oxide nanoparticles are commonly found in cosmetic products, and superparamagnetic iron oxide nanoparticles have been clinically exploited as contrast agents and anti-anemia medicines. As a result, human exposure to nanomaterials is continuously increasing, raising concerns about their potential adverse health effects. Historically, the study of nanoparticle toxicity has largely relied on macroscopic observations obtained in different in vitro and in vivo models, resulting in readouts such as median lethal dose, biodistribution profile, and/or histopathological assessment. In recent years, omics methodologies, including transcriptomics, epigenomics, proteomics, metabolomics, and lipidomics, are increasingly used to characterize the biological interactions of nanomaterials, providing a better and broader understanding of their impact and mechanisms of toxicity. These approaches have been able to identify important genes and gene products that mediate toxicological effects, as well as endogenous functions and pathways dysregulated by nanoparticles. Omics methods improve our understanding of nanoparticle biology, and unravel mechanistic insights into nanomedicine-based therapies. This review aims to provide a deeper understanding and new perspectives of omics approaches to characterize the toxicity and biological interactions of inorganic nanoparticles, and improve the safety of nanoparticle applications.

The mechanism of lovastatin in suppressing the proliferation of esophageal squamous cell carcinoma based on proteomics

BACKGROUND

Lovastatin, a type of statin usually considered as a lipid-lowering drug that lowers blood cholesterol and low-density lipoprotein cholesterol levels, has been rediscovered to have anticancer activity. Fewer studies exist regarding the effect of lovastatin on esophageal squamous cell carcinoma (ESCC).

METHODS

Here, we report that lovastatin shows anticancer effect on ESCC By affecting the mitochondrial autophagy pathway. Moreover, based on proteomics and computer molecular simulations found that RAB38 and RAB27A may be a target of lovastatin.

RESULTS

We observed that autophagy of mitochondria is inhibited by lovastatin, affecting esophageal squamous cell proliferation. There is a possible link between the expression of RAB38, RAB27A and immune cell invasion in esophageal cancer.

CONCLUSIONS

These results demonstrate the huge potential of lovastatin as an RAB38, RAB27A inhibitor in esophageal cancer chemotherapy and chemoprevention.

Biochemical analysis of Hyalomma dromedarii salivary glands and gut tissues using SR-FTIR micro-spectroscopy

Ticks are obligatory voracious blood feeders infesting diverse vertebrate hosts, that have a crucial role in the transmission of diverse pathogens that threaten human and animal health. The continuous emergence of tick-borne diseases due to combined worldwide climatic changes, human activities, and acaricide-resistant tick strains, necessitates the development of novel ameliorative tick control strategies such as vaccines. The synchrotron-based Fourier transform infrared micro-spectroscopy (SR-FTIR) is a bioanalytical microprobe capable of exploring the molecular chemistry within microstructures at a cellular or subcellular level and is considered as a nondestructive analytical approach for biological specimens. In this study, SR-FTIR analysis was able to explore a qualitative and semi-quantitative biochemical composition of gut and salivary glands of Hyalomma dromedarii (H. dromedarii) tick detecting differences in the biochemical composition of both tissues. A notable observation regarding Amide I secondary structure protein profile was the higher ratio of aggregated strands in salivary gland and beta turns in gut tissues. Regarding the lipid profile, there was a higher intensity of lipid regions in gut tissue when compared to salivary glands. This detailed information on the biochemical compositions of tick tissues could assist in selecting vaccine and/or control candidates. Altogether, these findings confirmed SR-FTIR spectroscopy as a tool for detecting differences in the biochemical composition of H. dromedarii salivary glands and gut tissues. This approach could potentially be extended to the analysis of other ticks that are vectors of important diseases such as babesiosis and theileriosis.

Peeking into the Stingers: A Comprehensive SWATH-MS Study of the European Hornet Vespa crabro (Linnaeus, 1758) (Hymenoptera: Vespidae) Venom Sac Extracts

This study aimed to investigate the venom sac extracts (VSEs) of the European hornet (EH) Vespa crabro (Linnaeus, 1758) (Hymenoptera: Vespidae), focusing on the differences between stinging females, gynes (G), and workers (W), at the protein level. Using a quantitative "Sequential Window Acquisition of all Theoretical Fragment Ion Mass Spectra" (SWATH-MS) analysis, we identified and quantified a total of 240 proteins. Notably, within the group, 45.8% (n = 110) showed significant differential expression between VSE-G and VSE-W. In this set, 57.3% (n = 63) were upregulated and 42.7% (n = 47) downregulated in the G. Additionally, the two-hundred quantified proteins from the class Insecta belong to sixteen different species, six of them to the Hymenoptera/Apidae lineage, comprising seven proteins with known potential allergenicity. Thus, phospholipase A1 (Vesp v 1), phospholipase A1 verutoxin 2b (VT-2b), hyaluronidase A (Vesp v 2A), hyaluronidase B (Vesp v 2B), and venom allergen 5 (Vesp v 5) were significantly downregulated in the G, and vitellogenin (Vesp v 6) was upregulated. Overall, 46% of the VSE proteins showed differential expression, with a majority being upregulated in G. Data are available via ProteomeXchange with identifier PXD047955. These findings shed light on the proteomic differences in VSE between EH castes, potentially contributing to our understanding of their behavior and offering insights for allergy research.

Uncovering the Hidden World of Aqueous Humor Proteins for Discovery of Biomarkers for Marfan Syndrome

Ectopia lentis is a hallmark of Marfan syndrome (MFS), a genetic connective tissue disorder affecting 1/5000 to 1/10 000 individuals worldwide. Early detection in ophthalmology clinics and timely intervention of cardiovascular complications can be lifesaving. In this study, a modified proteomics workflow with liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based data-independent acquisition (DIA) and field asymmetric ion mobility spectrometry (FAIMS) to profile the proteomes of aqueous humor (AH) and lens tissue from MFS children with ectopia lentis is utilized. Over 2300 and 2938 comparable proteins are identified in AH and the lens capsule, respectively. Functional enrichment analyses uncovered dysregulation of complement and coagulation-related pathways, collagen binding, and cell adhesion in MFS. Through weighted correlation network analysis (WGCNA) and machine learning, distinct modules associated with clinical traits are constructed and a unique biomarker panel (Q14376, Q99972, P02760, Q07507; gene names: GALE, MYOC, AMBP, DPT) is defined. These biomarkers are further validated using advanced parallel reaction monitoring (PRM) in an independent patient cohort. The results provide novel insights into the proteome characterization of ectopia lentis and offer a promising approach for developing a valuable biomarker panel to aid in the early diagnosis of Marfan syndrome via AH proteome.

Recent Advances in Metalloproteomics

Interactions between proteins and metal ions and their complexes are important in many areas of the life sciences, including physiology, medicine, and toxicology. Despite the involvement of essential elements in all major processes necessary for sustaining life, metalloproteomes remain ill-defined. This is not only owing to the complexity of metalloproteomes, but also to the non-covalent character of the complexes that most essential metals form, which complicates analysis. Similar issues may also be encountered for some toxic metals. The review discusses recently developed approaches and current challenges for the study of interactions involving entire (sub-)proteomes with such labile metal ions. In the second part, transition metals from the fourth and fifth periods are examined, most of which are xenobiotic and also tend to form more stable and/or inert complexes. A large research area in this respect concerns metallodrug-protein interactions. Particular attention is paid to separation approaches, as these need to be adapted to the reactivity of the metal under consideration.

Huanglian Ganjiang decoction alleviates ulcerative colitis by restoring gut barrier via APOC1-JNK/P38 MAPK signal pathway based on proteomic analysis

ETHNOPHARMACOLOGICAL RELEVANCE

Ulcerative colitis (UC) is a kind of chronic intestinal inflammation accompanied with abdominal pain, diarrhea and hematochezia. Huanglian Ganjiang decoction (HGD) derived from "Beiji Qianjin Yao Fang" was used for UC patients clinically. However, the specific mechanism of HGD in treating UC remain unclear.

AIM OF STUDY

Our study devoted to demonstrating the therapeutic effect of HGD for colitis and clarifying the underlying mechanism.

MATERIALS AND METHODS

UPLC-MS was carried out to identify the ingredients of HGD. UC mice were induced by giving 3% dextran sulfate sodium (DSS) solution for one week and treated by HGD for another week. Body weight fluctuation, disease activity index (DAI), colon length and pathological change of colon tissues were observed to evaluate therapeutical effect of HGD. ELISA and qPCR were carried out to estimate the inflammatory state. Western blot, qPCR and immunofluorescence were used to access the expression of tight junction proteins. Tandem mass tag (TMT)-Based proteomics and network pharmacology was launched to screen and predict the potential targets and pathway regulated by HGD.

RESULTS

Based on the UPLC-MS/MS analysis, 100 components were identified in HGD. After 7-day treatment, HGD significantly alleviated colitis-associated symptoms including body weight loss, shorted colon, increase of DAI score, histopathologic lesions. HGD also reduced inflammatory cytokines IL-6 and IL-1β levels, increased the number of goblet cells and restored tight junction proteins Occludin, Claudin-1 in colon. Network pharmacology study predicted that tight junction and MAPK pathway might be affected by HGD in colitis mice. APOC1 was screened out as key target in HGD-treated mice using TMT-based proteomics study. Further Western blot results showed that HGD reduced expressions of APOC1, p-P38 and p-JNK.

CONCLUSION

HGD improves general symptoms of colitis mice at medium and high doses, which may be associated with restoring tight junction and intestinal barrier integrity and function through suppression of APOC1-JNK/P38 MAPK signal pathway.

Application and discoveries of metabolomics and proteomics in the study of female infertility

Introduction

Female infertility is defined as the absence of clinical pregnancy after 12 months of regular unprotected sexual intercourse.

Methods

This study employed metabolomics and proteomics approaches to investigate the relationship between metabolites and proteins and female infertility. The study used metabolomics and proteomics data from the UK Biobank to identify metabolites and proteins linked to infertility.

Results

The results showed that GRAM domain-containing protein 1C and metabolites fibrinogen cleavage peptides ADpSGEGDFXAEGGGVR and 3-Hydroxybutyrate had a positive correlation with infertility, whereas proteins such as Interleukin-3 receptor subunit alpha, Thrombospondin type-1 domain-containing protein 1, Intestinal-type alkaline phosphatase, and platelet and endothelial cell adhesion molecule 1 exhibited a negative correlation. These findings provide new clues and targets for infertility diagnosis and treatment. However, further research is required to validate these results and gain a deeper understanding of the specific roles of these metabolites and proteins in infertility pathogenesis.

Discussion

In conclusion, metabolomics and proteomics techniques have significant application value in the study of infertility, allowing for a better understanding of the biological mechanisms underlying infertility and providing new insights and strategies for its diagnosis and treatment. These research findings provide a crucial biological mechanistic basis for early infertility screening, prevention, and treatment.

Proteomics and Metabolomics in Biomedicine

The technological advances of recent years have significantly enhanced medical discoveries [...].

Mass spectrometry as a lens into molecular human nutrition and health

Mass spectrometry (MS) has developed over the last decades into the most informative and versatile analytical technology in molecular and structural biology (). The platform enables discovery, identification, and characterisation of non-volatile biomolecules, such as proteins, peptides, DNA, RNA, nutrients, metabolites, and lipids at both speed and scale and can elucidate their interactions and effects. The versatility, robustness, and throughput have rendered MS a major research and development platform in molecular human health and biomedical science. More recently, MS has also been established as the central tool for 'Molecular Nutrition', enabling comprehensive and rapid identification and characterisation of macro- and micronutrients, bioactives, and other food compounds. 'Molecular Nutrition' thereby helps understand bioaccessibility, bioavailability, and bioefficacy of macro- and micronutrients and related health effects. Hence, MS provides a lens through which the fate of nutrients can be monitored along digestion via absorption to metabolism. This in turn provides the bioanalytical foundation for 'Personalised Nutrition' or 'Precision Nutrition' in which design and development of diets and nutritional products is tailored towards consumer and patient groups sharing similar genetic and environmental predisposition, health/disease conditions and lifestyles, and/or objectives of performance and wellbeing. The next level of integrated nutrition science is now being built as 'Systems Nutrition' where public and personal health data are correlated with life condition and lifestyle factors, to establish directional relationships between nutrition, lifestyle, environment, and health, eventually translating into science-based public and personal heath recommendations and actions. This account provides a condensed summary of the contributions of MS to a precise, quantitative, and comprehensive nutrition and health science and sketches an outlook on its future role in this fascinating and relevant field.

Proteomic profile of Trichinella spiralis infected mice with acute spinal cord injury: A 4D label-free quantitative analysis

Spinal cord injury (SCI) can cause severe loss of locomotor and sensory activities, with no ideal treatment. Emerging reports suggest that the helminth therapy is highly effective in relieving numerous inflammatory diseases. Proteomic profiling is often used to elucidate the underlying mechanism behind SCI. Herein, we systematically compared the protein expression profiles of murine SCI spinal cord and Trichinella spiralis treated murine SCI spinal cord, using a 4D label-free technique known for its elevated sensitivity. Relative to the SCI mice, the T. spiralis-treated mice exhibited marked alterations in 91 proteins (31 up- and 60 down-regulated). Based on our Gene Ontology (GO) functional analysis, the differentially expressed proteins (DEPs) were primarily enriched in the processes of metabolism, biological regulation, cellular process, antioxidant activity, and other cell functions. In addition, according to the Clusters of Orthologous Groups of protein/EuKaryotic Orthologous Groups (COG/KOG) functional stratification, proteins involved in signaling transduction mechanisms belonged to the largest category. Over-expressed DEPs were also enriched in the "NADPH oxidase complex", "superoxide anion generation", "other types of O-glycan biosynthesis", and "HIF-1 signaling pathway". Furthermore, the protein-protein interaction (PPI) network identified the leading 10 hub proteins. In conclusion, we highlighted the dynamic proteomic profiling of T. spiralis-treated SCI mice. Our findings provide significant insight into the molecular mechanism behind T. spiralis regulation of SCI.

A guide to mass spectrometric analysis of extracellular vesicle proteins for biomarker discovery

Exosomes (small extracellular vesicles) in living organisms play an important role in processes such as cell proliferation or intercellular communication. Recently, exosomes have been extensively investigated for biomarker discoveries for various diseases. An important aspect of exosome analysis involves the development of enrichment methods that have been introduced for successful isolation of exosomes. These methods include ultracentrifugation, size exclusion chromatography, polyethylene glycol-based precipitation, immunoaffinity-based enrichment, ultrafiltration, and asymmetric flow field-flow fractionation among others. To confirm the presence of exosomes, various characterization methods have been utilized such as Western blot analysis, atomic force microscopy, electron microscopy, optical methods, zeta potential, visual inspection, and mass spectrometry. Recent advances in high-resolution separations, high-performance mass spectrometry and comprehensive proteome databases have all contributed to the successful analysis of exosomes from patient samples. Herein we review various exosome enrichment methods, characterization methods, and recent trends of exosome investigations using mass spectrometry-based approaches for biomarker discovery.

Differential Expression of Serum Proteins in Chronic Obstructive Pulmonary Disease Assessed Using Label-Free Proteomics and Bioinformatics Analyses

PURPOSE

As a common respiratory disease, chronic obstructive pulmonary disease (COPD) has a high morbidity and mortality. Current clinical therapies are not ideal and do not improve lung function or long-term life quality. It is very important to find new potential pathogenic mechanisms, biomarkers, and targets with therapeutic value in COPD.

METHODS

Serum samples collected from acute exacerbation and stable COPD and healthy participants were analyzed using label-free liquid chromatography tandem mass spectrometry to identify the differentially expressed proteins (DEPs) between two groups. Bioinformatics analyses were performed to determine the biological processes associated with those DEPs. Key proteins were validated by enzyme linked immunosorbent assay (ELISA).

RESULTS

In total, 661 proteins were detected in serum from patients with COPD and healthy participants. Compared with healthy participants, patients with acute exacerbation of COPD had 45 DEPs, 13 were upregulated and 32 were downregulated; and patients with stable COPD had 79 DEPs, 18 were upregulated and 61 were downregulated. Gene Ontology functional annotation results indicated that the DEPs identified in patients with COPD were associated with the terms cellular anatomical entity, binding, and cellular process. Kyoto Encyclopedia of Genes and Genomes functional annotation analysis and the Clusters of Orthologous Genes database analysis indicated that the functions of these DEPs were primarily in signal transduction mechanisms and amino acid transport and metabolism. The ELISA results for three key proteins of IGFBP2, LRG1 and TAGLN were consistent with the LC-MS/MS results and the area under the receiver operating characteristic of the combined index was 0.893 (95% CI: 0.813, 0.974).

CONCLUSION

Our findings suggested pathogenic mechanisms underlying COPD stages and indicated three key proteins that may warrant further study as potential biomarkers for early diagnosis or prognosis of COPD or as therapeutic targets.

Prediction, Discovery, and Characterization of Plant- and Food-Derived Health-Beneficial Bioactive Peptides

Nature may have the answer to many of our questions about human, animal, and environmental health. Natural bioactives, especially when harvested from sustainable plant and food sources, provide a plethora of molecular solutions to nutritionally actionable, chronic conditions. The spectrum of these conditions, such as metabolic, immune, and gastrointestinal disorders, has changed with prolonged human life span, which should be matched with an appropriately extended health span, which would in turn favour more sustainable health care: "adding years to life and adding life to years". To date, bioactive peptides have been undervalued and underexploited as food ingredients and drugs. The future of translational science on bioactive peptides-and natural bioactives in general-is being built on (a) systems-level rather than reductionist strategies for understanding their interdependent, and at times synergistic, functions; and (b) the leverage of artificial intelligence for prediction and discovery, thereby significantly reducing the time from idea and concept to finished solutions for consumers and patients. This new strategy follows the path from benefit definition via design to prediction and, eventually, validation and production.