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Connecting Proteomics to Next-Generation Sequencing: Proteogenomics and Its Current Applications in Biology

Low TY, Mohtar MA, Ang MY, Jamal R

Proteomics, 2019 05;19(10):e1800235.
PMID: 30431238 DOI: 10.1002/pmic.201800235

Understanding the relationship between genotypes and phenotypes is essential to disentangle biological mechanisms and to unravel the molecular basis of diseases. Genes and proteins are closely linked in biological systems. However, genomics and proteomics have developed separately into two distinct disciplines whereby crosstalk among scientists from the two domains is limited and this constrains the integration of both fields into a single data modality of useful information. The emerging field of proteogenomics attempts to address this by building bridges between the two disciplines. In this review, how genomics and transcriptomics data in different formats can be utilized to assist proteogenomics application is briefly discussed. Subsequently, a much larger part of this review focuses on proteogenomics research articles that are published in the last five years that answer two important questions. First, how proteogenomics can be applied to tackle biological problems is discussed, covering genome annotation and precision medicine. Second, the latest developments in analytical technologies for data acquisition and the bioinformatics tools to interpret and visualize proteogenomics data are covered.

Matched MeSH terms: Tandem Mass Spectrometry
Fulltext Residual quantification and oxidative stress induced by malachite green after subacute and sublethal exposure in red tilapia

Kwan PP, Banerjee S, Shariff M, Yusoff FM

Vet World, 2019 Sep;12(9):1416-1421.
PMID: 31749575 DOI: 10.14202/vetworld.2019.1416-1421

Background and Aim: Malachite green (MG) is an effective antiparasitic and antifungal chemical for treatment of fish. However, MG is reported to be a potential carcinogen. Yet, it is widely used in aquaculture despite its prohibition for use in food-producing animals by the EU and USFDA. The present study quantified MG residues and evaluated the oxidative stress in red tilapia when exposed to subacute and sublethal concentrations of MG.
Materials and Methods: Red tilapia exposed to subacute (0.105 mg/L for 20 days) and sublethal (0.053 mg/L for 60 days) concentrations were evaluated for total plasma protein, total immunoglobulin, nitroblue tetrazolium activity, malondialdehyde, reduced glutathione (GSH), and catalase (CAT) activity levels. The residues of MG and leuco-MG (LMG) were also quantified in the fish muscles using liquid chromatography-tandem mass spectrometry.
Results: Fish exposed to subacute concentration showed higher CAT on day 10 in the liver and days 5 and 15 in the spleen, whereas in fish exposed to the sublethal concentration, higher levels of GSH were observed on day 1 in the kidney and day 50 in the spleen. Fish muscle was able to accumulate the sum of MG and LMG of 108.04 µg/kg for subacute (day 20) and 82.68 µg/kg for sublethal (day 60).
Conclusion: This study showed that red tilapia was able to adapt to the stress caused by exposure to MG at sublethal concentration.

Matched MeSH terms: Tandem Mass Spectrometry
Phyllanthus amarus protects against spatial memory impairment induced by lipopolysaccharide in mice

Alagan A, Jantan I, Kumolosasi E, Azmi N

Bioinformation, 2019;15(8):535-541.
PMID: 31719762 DOI: 10.6026/97320630015535

Phyllanthus amarus Schumach. and Thonn. is a wide spread medicinal herb with various traditional uses. It is well documented for its antioxidant, anti-inflammatory, and hepatoprotective activities. Therefore, it is of interest to evaluate the 80% ethanol extract of Phyllanthus amarus (PA) on spatial memory using the 8-radial arm maze (8-RAM) in mice after induction of neuro inflammation by lipopolysaccharide (LPS) in a 14- and 28-days treatment study. LC-MS/MS was performed to profile the chemical composition in PA extract. Mice were treated orally with 5% v/v tween 20, PA extract (100, 200 and 400 mg/kg), or ibuprofen (IBF 40 mg/kg) for 14 and 28 days. All groups were challenged with LPS (1 mg/kg) via intraperitoneal (i.p.) injection a day prior to the 8-RAM task except for the negative control group which received an i.p. injection of saline. Data obtained were analyzed with one-way ANOVA followed by post hoc Dunnett's test (comparison of all groups against vehicle control). Analysis of LC-MS/MS data revealed the presence of 16 compounds in the PA extract. Administration of PA extract at 200 and 400 mg/kg for 14 and 28 days significantly (*P<0.05) decreased the working and reference memory errors against LPS-induced spatial memory impairment. The observed protective action is possibly due to the putative antineuroinflammatory effects of PA. In conclusion, PA extract possess neuroprotective effects against spatial memory impairment mediated by LPS.

Matched MeSH terms: Tandem Mass Spectrometry
Comparison assessment between SIM and MRM mode in the analysis of 3-MCPD ester, 2-MCPD ester and glycidyl ester

Goh KM, Wong YH, Ang MY, Yeo SCM, Abas F, Lai OM, et al.

Food Res Int, 2019 07;121:553-560.
PMID: 31108780 DOI: 10.1016/j.foodres.2018.12.013

The detection of 3- and 2-MCPD ester and glycidyl ester was transformed from selected ion monitoring (SIM) mode to multiple reaction monitoring (MRM) mode by gas chromatography triple quadrupole spectrometry. The derivatization process was adapted from AOCS method Cd 29a-13. The results showed that the coefficient of determination (R2) of all detected compounds obtained from both detection mode was comparable, which falls between 0.997 and 0.999. The limit of detection and quantification (LOD and LOQ) were improved in MRM mode as compared to SIM mode. In MRM mode, the LOD of 3- and 2-MCPD ester was achieved 0.01 mg/kg while the LOQ was 0.05 mg/kg. Besides, LOD and LOQ of glycidyl ester were 0.024 and 0.06 mg/kg respectively. A blank spiked with MCPD esters (0.03, 0.10 and 0.50 mg/kg) and GE (0.06, 0.24 and 1.20 mg/kg) were chosen for repeatability and recovery tests. MRM mode showed better repeatability in area ratio and recovery with relative standard deviation (RSD %) 

Matched MeSH terms: Tandem Mass Spectrometry
Changes in hepatic phosphoprotein levels in mice infected with Plasmodium berghei

Maniam P, Zainal Abidin Abu Hassan, Noor Embi, Hasidah Mohd Sidek

Sains Malaysiana, 2012;41:721-729.

Hepatic phosphoprotein levels are altered in mouse liver as a manifestation of bacteria, virus or parasite infection. Identification of signaling pathways mediated by these hepatic proteins contribute to the current understanding of the mechanism of pathogenesis in malarial infection. The present study was undertaken to evaluate the changes in hepatic phosphoprotein levels during Plasmodium berghei infection. Our study revealed changes in levels of three hepatic phosphoproteins following P. berghei infection compared to non-infected controls. Peptide fragment sequence analysis using tandem mass spectrometry (MS/MS) showed these hepatic proteins to be homologs to haemoglobin beta (HBB), class
Pi glutathione S-tranferase (GSTPi) and carbonic anhydrase III (CAIII) proteins of Mus musculus species respectively from the NCBInr sequence database. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis predicted the involvement of these proteins in specific pathways in Mus musculus species; GSTPi in glutathione and drug metabolism and CAIII in nitrogen metabolism. This shows that P. berghei infection affects similar signaling pathways as those reported in other pathogenic infections such as that related to GSTPi and CAIII in response to oxidative stress.

Matched MeSH terms: Tandem Mass Spectrometry
Quantitation of Protein Cysteine-Phenol Adducts in Minced Beef Containing 4-Methyl Catechol

Arsad SS, Zainudin MAM, De Gobba C, Jongberg S, Larsen FH, Lametsch R, et al.

J Agric Food Chem, 2020 Feb 26;68(8):2506-2515.
PMID: 32013414 DOI: 10.1021/acs.jafc.9b07752

Thiol groups of cysteine (Cys) residues in proteins react with quinones, oxidation products of polyphenols, to form protein-polyphenol adducts. The aim of the present work was to quantify the amount of adduct formed between Cys residues and 4-methylcatechol (4MC) in minced beef. A Cys-4MC adduct standard was electrochemically synthesized and characterized by liquid chromatography-mass spectrometry (LC-MS) as well as NMR spectroscopy. Cys-4MC adducts were quantified after acidic hydrolysis of myofibrillar protein isolates (MPIs) and LC-MS/MS analysis of meat containing either 500 or 1500 ppm 4MC and stored at 4 °C for 7 days under a nitrogen or oxygen atmosphere. The concentrations of Cys-4MC were found to be 2.2 ± 0.3 nmol/mg MPI and 8.1 ± 0.9 nmol/mg MPI in meat containing 500 and 1500 ppm 4MC, respectively, and stored for 7 days under oxygen. The formation of the Cys-4MC adduct resulted in protein thiol loss, and ca. 62% of the thiol loss was estimated to account for the formation of the Cys-4MC adduct for meat containing 1500 ppm 4MC. Furthermore, protein polymerization increased in samples containing 4MC as evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and the polymerization was found to originate from protein-polyphenol interactions as evaluated by a blotting assay with staining by nitroblue tetrazolium.

Matched MeSH terms: Tandem Mass Spectrometry
Proteomes of the female salivary glands of Simulium nigrogilvum and Simulium nodosum, the main human-biting black flies in Thailand

Hempolchom C, Reamtong O, Sookrung N, Srisuka W, Sakolvaree Y, Chaicumpa W, et al.

Acta Trop, 2019 Jun;194:82-88.
PMID: 30922801 DOI: 10.1016/j.actatropica.2019.03.026

Although several studies have reported pharmacological and immunological activity, as well as the role of black flies in transmitting pathogens to vertebrate hosts through salivary glands (SG) during blood feeding, SG proteomes of the anthropophilic black flies in Thailand have never been reported. Therefore, this study determined the SG proteomes of female S. nigrogilvum and S. nodosum. Sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional (2-DE) gels containing separated SG proteins of individual species were subjected to liquid chromatography-tandem mass spectrometry (LCMS/MS) and an orthologous protein search from eukaryotic organism, nematocera and simuliidae databases for total protein identification. SDS-PAGE and protein staining revealed at least 13 and 9 major protein bands in the SGs of female S. nigrogilvum and S. nodosum, respectively, as well as several minor ones. The 2-DE demonstrated a total of 56 and 41 protein spots for S. nigrogilvum and S. nodosum, respectively. Most of the proteins obtained in both species were enzymes involved in blood feeding, including proteases, apyrases, hyaluronidases, aminopeptidase and elastase. The results obtained in this study provided a new body of knowledge for a better understanding on the role of salivary gland proteins in these black fly species in Thailand.

Matched MeSH terms: Tandem Mass Spectrometry
Fulltext Strontium Sulfite: A New pH-Responsive Inorganic Nanocarrier to Deliver Therapeutic siRNAs to Cancer Cells

Karim ME, Shetty J, Islam RA, Kaiser A, Bakhtiar A, Chowdhury EH

Pharmaceutics, 2019 Feb 20;11(2).
PMID: 30791612 DOI: 10.3390/pharmaceutics11020089

Inorganic nanoparticles hold great potential in the area of precision medicine, particularly for treating cancer owing to their unique physicochemical properties, biocompatibility and improved pharmacokinetics properties compared to their organic counterparts. Here we introduce strontium sulfite nanoparticles as new pH-responsive inorganic nanocarriers for efficient transport of siRNAs into breast cancer cells. We employed the simplest nanoprecipitation method to generate the strontium sulfite nanoparticles (SSNs) and demonstrated the dramatic roles of NaCl and d-glucose in particle growth stabilization in order to produce even smaller nanosize particles (Na-Glc-SSN) with high affinity towards negatively charged siRNA, enabling it to efficiently enter the cancer cells. Moreover, the nanoparticles were found to be degraded with a small drop in pH, suggesting their potential capability to undergo rapid dissolution at endosomal pH so as to release the payload. While these particles were found to be nontoxic to the cells, they showed higher potency in facilitating cancer cell death through intracellular delivery and release of oncogene-specific siRNAs targeting ros1 and egfr1 mRNA transcripts, than the strontium sulfite particles prepared in absence of NaCl and d-glucose, as confirmed by growth inhibition assay. The mouse plasma binding analysis by Q-TOF LC-MS/MS demonstrated less protein binding to smaller particles of Na-Glc-SSNs. The biodistribution studies of the particles after 4 h of treatment showed Na-Glc-SSNs had less off-target distribution than SSNs, and after 24 h, all siRNAs were cleared from all major organs except the tumors. ROS1 siRNA with its potential therapeutic role in treating 4T1-induced breast tumor was selected for subsequent in vivo tumor regression study, revealing that ROS1 siRNA-loaded SSNs exerted more significant anti-tumor effects than Na-Glc-SSNs carrying the same siRNA following intravenous administration, without any systemic toxicity. Thus, strontium sulfite emerged as a powerful siRNA delivery tool with potential applications in cancer gene therapy.

Matched MeSH terms: Tandem Mass Spectrometry
Identification of angiotensin-converting enzyme inhibitory proteins from mycelium of Pleurotus pulmonarius (oyster mushroom)

Ibadallah BX, Abdullah N, Shuib AS

Planta Med, 2015 Jan;81(2):123-9.
PMID: 25590365 DOI: 10.1055/s-0034-1383409

Pleurotus pulmonarius (grey oyster mushroom) has been acknowledged as a recuperative agent for many diseases in addition to its recognition as a nutritious provision. We performed a study on P. pulmonarius mycelium for an antihypertensive effect via the angiotensin-converting enzyme inhibitory activity. The preliminary assay on the mycelial water extract demonstrated that the angiotensin-converting enzyme inhibitory activity had an IC50 value of 720 µg/mL. Further protein purifications via ammonium sulphate precipitation and RP-HPLC resulted in 60× stronger angiotensin-converting enzyme inhibitory activity than that of the mycelial water extract (IC50 = 12 µg/mL). Protein identification and characterisation by MALDI-TOF/TOF, later corroborated by LC-MS/MS, indicated three proteins that are responsible for the blood pressure lowering effects via different mechanisms: serine proteinase inhibitor-like protein, nitrite reductase-like protein, and DEAD/DEAH box RNA helicase-like protein.

Matched MeSH terms: Tandem Mass Spectrometry
Discovery of Antimalarial Drugs from Streptomycetes Metabolites Using a Metabolomic Approach

Ahmad SJ, Abdul Rahim MBH, Baharum SN, Baba MS, Zin NM

J Trop Med, 2017;2017:2189814.
PMID: 29123551 DOI: 10.1155/2017/2189814

Natural products continue to play an important role as a source of biologically active substances for the development of new drug. Streptomyces, Gram-positive bacteria which are widely distributed in nature, are one of the most popular sources of natural antibiotics. Recently, by using a bioassay-guided fractionation, an antimalarial compound, Gancidin-W, has been discovered from these bacteria. However, this classical method in identifying potentially novel bioactive compounds from the natural products requires considerable effort and is a time-consuming process. Metabolomics is an emerging "omics" technology in systems biology study which integrated in process of discovering drug from natural products. Metabolomics approach in finding novel therapeutics agent for malaria offers dereplication step in screening phase to shorten the process. The highly sensitive instruments, such as Liquid Chromatography-Mass Spectrophotometry (LC-MS), Gas Chromatography-Mass Spectrophotometry (GC-MS), and Nuclear Magnetic Resonance ((1)H-NMR) spectroscopy, provide a wide range of information in the identification of potentially bioactive compounds. The current paper reviews concepts of metabolomics and its application in drug discovery of malaria treatment as well as assessing the antimalarial activity from natural products. Metabolomics approach in malaria drug discovery is still new and needs to be initiated, especially for drug research in Malaysia.

Matched MeSH terms: Tandem Mass Spectrometry
Fulltext First evidence for a multienzyme complex of lipid biosynthesis pathway enzymes in Cunninghamella bainieri

Shuib S, Ibrahim I, Mackeen MM, Ratledge C, Hamid AA

Sci Rep, 2018 Feb 15;8(1):3077.
PMID: 29449592 DOI: 10.1038/s41598-018-21452-4

Malic enzyme (ME) plays a vital role in determining the extent of lipid accumulation in oleaginous fungi being the major provider of NADPH for the activity of fatty acid synthase (FAS). We report here the first direct evidence of the existence of a lipogenic multienzyme complex (the lipid metabolon) involving ME, FAS, ATP: citrate lyase (ACL), acetyl-CoA carboxylase (ACC), pyruvate carboxylase (PC) and malate dehydrogenase (MDH) in Cunninghamella bainieri 2A1. Cell-free extracts prepared from cells taken in both growth and lipid accumulation phases were prepared by protoplasting and subjected to Blue Native (BN)-PAGE coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). A high molecular mass complex (approx. 3.2 MDa) consisting of the above enzymes was detected during lipid accumulation phase indicating positive evidence of multienzyme complex formation. The complex was not detected in cells during the balanced phase of growth or when lipid accumulation ceased, suggesting that it was transiently formed only during lipogenesis.

Matched MeSH terms: Tandem Mass Spectrometry
Level of natural hepatotoxin (Indospicine) contamination in Australian camel meat

Tan ET, Al Jassim R, D'Arcy BR, Fletcher MT

Food Addit Contam Part A Chem Anal Control Expo Risk Assess, 2016 Oct;33(10):1587-1595.
PMID: 27575484

Camel meat production for human consumption and pet food manufacture accounts for a relatively small part of overall red meat production in Australia. Reliable statistical data for the Australian production and consumption of camel meat are not available; however, it is estimated that 300,000 feral camels roam within the desert of central Australia, with an annual usage of more than 3000 camels for human consumption, 2000 for pet food manufacture and a smaller number for live export. Despite a small Australian camel meat production level, the usage of camel meat for pet food has been restricted in recent years due to reports of serious liver disease and death in dogs consuming camel meat. This camel meat was found to contain residues of indospicine, a non-proteinogenic amino acid found in certain Indigofera spp., and associated with mild to severe liver disease in diverse animals after dietary exposure to this hepatotoxin. The extent of indospicine-contaminated Australian camel meat was previously unknown, and this study ascertains the prevalence of such residue in Australian camel meat. In this study, indospicine levels in ex situ (95 samples collected from an abattoir in Queensland) and in situ (197 samples collected from camels after field culling in central Australia) camel meat samples were quantitated using a validated ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The quantitation results showed 46.7% of the in situ- and 20.0% of the ex situ-collected camel meat samples were contaminated by indospicine (more than the limit of detection (LOD) of 0.05 mg kg(-1) fresh weight). The overall indospicine concentration was higher (p < 0.05) in the in situ-collected samples. Indospicine levels detected in the present study are considered to be low; however, a degree of caution must still be exercised, since the tolerable daily intake for indospicine is currently not available for risk estimation.

Matched MeSH terms: Tandem Mass Spectrometry
Fulltext Comparative proteomics reveals that YK51, a 4-Hydroxypandurantin-A analogue, downregulates the expression of proteins associated with dengue virus infection

Tan WL, Lee YK, Ho YF, Yusof R, Abdul Rahman N, Karsani SA

PeerJ, 2018;5:e3939.
PMID: 29404200 DOI: 10.7717/peerj.3939

Dengue is endemic throughout tropical and subtropical regions of the world. Currently, there is no clinically approved therapeutic drug available for this acute viral infection. Although the first dengue vaccine Dengvaxia has been approved for use in certain countries, it is limited to those without a previous dengue infection while the safety and efficacy of the vaccine in those elderly and younger children still need to be identified. Therefore, it is becoming increasingly important to develop therapeutics/drugs to combat dengue virus (DENV) infection. YK51 is a synthetic analogue of 4-Hydroxypandurantin A (a compound found in the crude extract of the rhizomes of Boesenbergia rotunda) that has been extensively studied by our research group. It has been shown to possess outstanding antiviral activity due to its inhibitory activity against NS2B/NS3 DENV2 protease. However, it is not known how YK51 affects the proteome of DENV infected cells. Therefore, we performed a comparative proteomics analysis to identify changes in protein expression in DENV infected HepG2 cells treated with YK51. Classical two-dimensional gel electrophoresis followed by protein identification using tandem mass spectrometry was employed in this study. Thirty proteins were found to be down-regulated with YK51 treatment. In silico analysis predicted that the down-regulation of eight of these proteins may inhibit viral infection. Our results suggested that apart from inhibiting the NS2B/NS3 DENV2 protease, YK51 may also be causing the down-regulation of a number of proteins that may be responsible in, and/or essential to virus infection. However, functional characterization of these proteins will be necessary before we can conclusively determine their roles in DENV infection.

Matched MeSH terms: Tandem Mass Spectrometry
Simultaneous formation of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatic amines (HCAs) in gas-grilled beef satay at different temperatures

Ahmad Kamal NH, Selamat J, Sanny M

Food Addit Contam Part A Chem Anal Control Expo Risk Assess, 2018 May;35(5):848-869.
PMID: 29334335 DOI: 10.1080/19440049.2018.1425553

This study investigated the simultaneous formation of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatic amines (HCAs) in gas-grilled beef satay at different temperatures (150, 200, 250, 300, and 350°C). Solid-phase extraction (SPE) was used for sample clean-up. Fifteen PAHs were determined using high performance liquid chromatography with fluorescence detection (HPLC-FLD) and nine HCAs were quantified using liquid chromatography tandem-mass spectrometry (LC-MS/MS) with a gradient programme. The lowest significantly concentrations of PAHs and HCAs were generated at 150°C; the formation of PAHs and HCAs simultaneously increased with temperatures. Benzo[a]pyrene was detected in all samples and increased markedly at 300 and 350°C. The sums of 4 PAHs (PAH4) in marinated beef satay at 300 and 350°C exceeded the maximum level in Commission Regulation (EU) 2015/1125. Significant reductions of polar and non-polar HCAs (except PhIP) were found in marinated beef satay across all temperatures. Overall, PAHs and HCAs showed opposite trends of formation in beef satay with marination.

Matched MeSH terms: Tandem Mass Spectrometry
Fulltext Metabolomic analysis of low and high biofilm-forming Helicobacter pylori strains

Wong EHJ, Ng CG, Goh KL, Vadivelu J, Ho B, Loke MF

Sci Rep, 2018 01 23;8(1):1409.
PMID: 29362474 DOI: 10.1038/s41598-018-19697-0

The biofilm-forming-capability of Helicobacter pylori has been suggested to be among factors influencing treatment outcome. However, H. pylori exhibit strain-to-strain differences in biofilm-forming-capability. Metabolomics enables the inference of spatial and temporal changes of metabolic activities during biofilm formation. Our study seeks to examine the differences in metabolome of low and high biofilm-formers using the metabolomic approach. Eight H. pylori clinical strains with different biofilm-forming-capability were chosen for metabolomic analysis. Bacterial metabolites were extracted using Bligh and Dyer method and analyzed by Liquid Chromatography/Quadrupole Time-of-Flight mass spectrometry. The data was processed and analyzed using the MassHunter Qualitative Analysis and the Mass Profiler Professional programs. Based on global metabolomic profiles, low and high biofilm-formers presented as two distinctly different groups. Interestingly, low-biofilm-formers produced more metabolites than high-biofilm-formers. Further analysis was performed to identify metabolites that differed significantly (p-value

Matched MeSH terms: Tandem Mass Spectrometry
Proteomics Identification of Potential Candidates Involved in Cell Proliferation for Early Stage of Brain Regeneration in the Adult Zebrafish

Lim FT, Ogawa S, Smith AI, Parhar IS

Zebrafish, 2017 Feb;14(1):10-22.
PMID: 27797681 DOI: 10.1089/zeb.2016.1319

The central nervous system (CNS) of the non-mammalian vertebrates has better neuroregenerative capability as compared with the mammalian CNS. Regeneration of habenula was observed 40 days after damage in zebrafish. During the early stage of regeneration, we found a significant increase of apoptotic cells on day-1 post-damage and of proliferative cells on day-3 post-damage. To identify the molecular factor(s) involved in the early stages of neuroregeneration, differentially expressed proteins during sham, 20- and 40-h post-habenula damage were investigated by proteomic approach by using two-dimensional differential gel electrophoresis (2D-DIGE) coupled with Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight (MALDI-ToF) and tandem mass spectrometry. Protein profiles revealed 17 differentially (>1.5-fold) expressed proteins: 10 upregulated, 4 downregulated, 2 proteins were found to be downregulated at the early stage but upregulated at a later stage, and 1 protein was found to be upregulated at 2 different time points. All proteins identified can be summarized under few molecular processes involved in the early stages of neuroregeneration in zebrafish CNS: apoptosis regulation (Wnt inhibitory factor 1 [WIF1]), neuroprotection (metallothionein), cell proliferation (Spred2, ependymin, Lhx1, and Wnts), differentiation (Spred2, Lhx9, and Wnts), and morphogenesis (cytoplasmic actins and draculin). These protein profiling results suggest that drastic molecular changes occur in the neuroregenerative process during this period, which includes cell proliferation, differentiation, and protection.

Matched MeSH terms: Tandem Mass Spectrometry
Panel of serum protein biomarkers to grade the severity of traumatic brain injury

Anada RP, Wong KT, Jayapalan JJ, Hashim OH, Ganesan D

Electrophoresis, 2018 09;39(18):2308-2315.
PMID: 29570807 DOI: 10.1002/elps.201700407

The Glasgow Coma Scale (GCS), which classifies patients into mild, moderate or severe traumatic brain injury (TBI), is a system used to prioritize treatment and prognosticate the severity of head injury. In this study, sera of patients with various stages of TBI, as well as control subjects, were analyzed to screen for proteins that may be used to complement the GCS system. By subjecting pooled serum samples to iTRAQ analysis for quantitative comparison of protein abundance, and attesting their altered levels using ELISA, we have detected increased levels of serum amyloid A, C-reactive protein, leucine-rich alpha-2-glycoprotein, lipopolysaccharide-binding protein, fibronectin, vitronectin and alpha-1-antichymotrypsin in patients across all strata of TBI relative to the controls. However, kininogen was decreased only in moderate and severe TBI, whereas apolipoprotein E and zinc-alpha-2-glycoprotein were only increased in severe TBI. Hence, we propose a panel of serum biomarkers, which if analyzed within 24 h of the injury, can be used to diagnose patients with TBI into mild, moderate or severe stratification objectively, thus complementing the traditional GCS.

Matched MeSH terms: Tandem Mass Spectrometry
Fulltext The Effects of Drying Techniques on Phytochemical Contents and Biological Activities on Selected Bamboo Leaves

Benjamin MAZ, Ng SY, Saikim FH, Rusdi NA

Molecules, 2022 Sep 30;27(19).
PMID: 36234995 DOI: 10.3390/molecules27196458

The therapeutic potential of bamboos has acquired global attention. Nonetheless, the biological activities of the plants are rarely considered due to limited available references in Sabah, Malaysia. Furthermore, the drying technique could significantly affect the retention and degradation of nutrients in bamboos. Consequently, the current study investigated five drying methods, namely, sun, shade, microwave, oven, and freeze-drying, of the leaves of six bamboo species, Bambusa multiplex, Bambusa tuldoides, Bambusa vulgaris, Dinochloa sublaevigata, Gigantochloa levis, and Schizostachyum brachycladum. The infused bamboo leaves extracts were analysed for their total phenolic content (TPC) and total flavonoid content (TFC). The antioxidant activities of the samples were determined via the 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and ferric reducing antioxidant power (FRAP) assays, whereas their toxicities were evaluated through the brine shrimp lethality assay (BSLA). The chemical constituents of the samples were determined using liquid chromatography−tandem mass spectrometry (LC-MS/MS). The freeze-drying method exhibited the highest phytochemical contents and antioxidant activity yield, excluding the B. vulgaris sample, in which the microwave-dried sample recorded the most antioxidant and phytochemical levels. The TPC and TFC results were within the 2.69 ± 0.01−12.59 ± 0.09 mg gallic acid equivalent (GAE)/g and 0.77 ± 0.01−2.12 ± 0.01 mg quercetin equivalent (QE)/g ranges, respectively. The DPPH and ABTS IC50 (half-maximal inhibitory concentration) were 2.92 ± 0.01−4.73 ± 0.02 and 1.89−0.01 to 3.47 ± 0.00 µg/mL, respectively, indicating high radical scavenging activities. The FRAP values differed significantly between the drying methods, within the 6.40 ± 0.12−36.65 ± 0.09 mg Trolox equivalent (TE)/g range. The phytochemical contents and antioxidant capacities exhibited a moderate correlation, revealing that the TPC and TFC were slightly responsible for the antioxidant activities. The toxicity assessment of the bamboo extracts in the current study demonstrated no toxicity against the BSLA based on the LC50 (lethal concentration 50) analysis at >1000 µg/mL. LC-MS analysis showed that alkaloid and pharmaceutical compounds influence antioxidant activities, as found in previous studies. The acquired information might aid in the development of bamboo leaves as functional food items, such as bamboo tea. They could also be investigated for their medicinal ingredients that can be used in the discovery of potential drugs.

Matched MeSH terms: Tandem Mass Spectrometry
Ozonation of metoprolol in aqueous solution: ozonation by-products and mechanisms of degradation

Tay KS, Rahman NA, Abas MR

Environ Sci Pollut Res Int, 2013 May;20(5):3115-21.
PMID: 23054788 DOI: 10.1007/s11356-012-1223-3

This study investigated the degradation pathway of metoprolol, a widely used β-blocker, in the ozonation via the identification of generated ozonation by-products (OPs). Structure elucidation of OPs was performed using HPLC coupled with quadrupole time-of-flight high-resolution mass spectrometry. Seven OPs were identified, and four of these have not been reported elsewhere. Identified OPs of metoprolol included aromatic ring breakdown by-products; aliphatic chain degraded by-products and aromatic ring mono-, di-, and tetrahydroxylated derivatives. Based on the detected OPs, metoprolol could be degraded through aromatic ring opening reaction via reaction with ozone (O3) and degradation of aliphatic chain and aromatic ring via reaction with hydroxyl radical (•OH).

Matched MeSH terms: Tandem Mass Spectrometry
Platanosides from Platanus × acerifolia: New molecules, SAR, and target validation of a strong lead for drug-resistant bacterial infections and the associated sepsis

Wu XY, Zhao ZY, Osman EEA, Wang XJ, Choo YM, Benjamin MM, et al.

Bioorg Chem, 2024 Feb;143:107103.
PMID: 38211549 DOI: 10.1016/j.bioorg.2024.107103

Three undescribed (1-3) and nine known (4-12) platanosides were isolated and characterized from a bioactive extract of the May leaves of Platanus × acerifolia that initially showed inhibition against Staphylococcus aureus. Targeted compound mining was guided by an LC-MS/MS-based molecular ion networking (MoIN) strategy combined with conventional isolation procedures from a unique geographic location. The novel structures were mainly determined by 2D NMR and computational (NMR/ECD calculations) methods. Compound 1 is a rare acylated kaempferol rhamnoside possessing a truxinate unit. 6 (Z,E-platanoside) and 7 (E,E-platanoside) were confirmed to have remarkable inhibitory effects against both methicillin-resistant S. aureus (MIC: ≤ 16 μg/mL) and glycopeptide-resistant Enterococcus faecium (MIC: ≤ 1 μg/mL). These platanosides were subjected to docking analyses against FabI (enoyl-ACP reductase) and PBP1/2 (penicillin binding protein), both of which are pivotal enzymes governing bacterial growth but not found in the human host. The results showed that 6 and 7 displayed superior binding affinities towards FabI and PBP2. Moreover, surface plasmon resonance studies on the interaction of 1/7 and FabI revealed that 7 has a higher affinity (KD = 1.72 μM), which further supports the above in vitro data and is thus expected to be a novel anti-antibacterial drug lead.

Matched MeSH terms: Tandem Mass Spectrometry

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