Molecules

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17 pages, 2603 KiB

Open AccessArticle

Comparative Proteomic Analysis of Drug Trichosanthin Addition to BeWo Cell Line

by Yajun Hu, Jun Yao, Zening Wang, Hui Liang, Cunyu Li, Xinwen Zhou, Fengying Yang, Yang Zhang and Hong Jin

Molecules 2022, 27(5), 1603; https://doi.org/10.3390/molecules27051603 - 28 Feb 2022

Cited by 3 | Viewed by 1945

Abstract

Trichosanthin (TCS) is a traditional Chinese herbal medicine used to treat some gynecological diseases. Its effective component has diverse biological functions, including antineoplastic activity. The human trophoblast cell line BeWo was chosen as an experimental model for in vitro testing of a drug [...] Read more.

Trichosanthin (TCS) is a traditional Chinese herbal medicine used to treat some gynecological diseases. Its effective component has diverse biological functions, including antineoplastic activity. The human trophoblast cell line BeWo was chosen as an experimental model for in vitro testing of a drug screen for anticancer properties of TCS. The MTT method was used in this study to get a primary screen result. The result showed that 100 mM had the best IC₅₀ value. Proteomics analysis was then performed for further investigation of the drug effect of TCS on the BeWo cell line. In this differential proteomic expression analysis, the total proteins extracted from the BeWo cell line and their protein expression level after the drug treatment were compared by 2DE. Then, 24 unique three-fold differentially expressed proteins (DEPs) were successfully identified by MALDI-TOF/TOF MS. Label-free proteomics was run as a complemental method for the same experimental procedure. There are two proteins that were identified in both the 2DE and label-free methods. Among those identified proteins, bioinformatics analysis showed the importance of pathway and signal transduction and gives us the potential possibility for the disease treatment hypothesis. Full article

(This article belongs to the Special Issue Mass Spectrometry Analysis)

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12 pages, 9328 KiB

Open AccessArticle

A Pilot Study of Rare Renal Amyloidosis Based on FFPE Proteomics

by Shuang Meng, Wenwen Xia, Li Xia, Li Zhou, Jing Xu, Xiaoxia Pan and Liyuan Meng

Molecules 2021, 26(23), 7234; https://doi.org/10.3390/molecules26237234 - 29 Nov 2021

Cited by 3 | Viewed by 1995

Abstract

Renal amyloidosis typically manifests albuminuria, nephrotic-range proteinuria, and ultimately progresses to end-stage renal failure if diagnosed late. Different types of renal amyloidosis have completely different treatments and outcomes. Therefore, amyloidosis typing is essential for disease prognosis, genetic counseling and treatment. Thirty-six distinct proteins [...] Read more.

Renal amyloidosis typically manifests albuminuria, nephrotic-range proteinuria, and ultimately progresses to end-stage renal failure if diagnosed late. Different types of renal amyloidosis have completely different treatments and outcomes. Therefore, amyloidosis typing is essential for disease prognosis, genetic counseling and treatment. Thirty-six distinct proteins currently known to cause amyloidosis that have been described as amyloidogenic precursors, immunohistochemistry (IHC) or immunofluorescence (IF), can be challenging for amyloidosis typing especially in rare or hereditary amyloidosis in clinical practice. We made a pilot study that optimized the proteomics pre-processing procedures for trace renal amyloidosis formalin-fixed paraffin-embedded (FFPE) tissue samples, combined with statistical and bioinformatics analysis to screen out the amyloidosis-related proteins to accurately type or subtype renal amyloidosis in order to achieve individual treatment. A sensitive, specific and reliable FFPE-based proteomics analysis for trace sample manipulation was developed for amyloidosis typing. Our results not only underlined the great promise of traditional proteomics and bioinformatics analysis using FFPE tissues for amyloidosis typing, but also proved that retrospective diagnosis and analysis of previous cases laid a solid foundation for personalized treatment. Full article

(This article belongs to the Special Issue Mass Spectrometry Analysis)

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11 pages, 1899 KiB

Open AccessArticle

Metabolomic Characterization of Cerebrospinal Fluid from Intracranial Bacterial Infection Pediatric Patients: A Pilot Study

by Yiwen Wang, Yu Liu, Ruoping Chen and Liang Qiao

Molecules 2021, 26(22), 6871; https://doi.org/10.3390/molecules26226871 - 15 Nov 2021

Cited by 7 | Viewed by 2582

Abstract

Intracranial bacterial infection remains a major cause of morbidity and mortality in neurosurgical cases. Metabolomic profiling of cerebrospinal fluid (CSF) holds great promise to gain insights into the pathogenesis of central neural system (CNS) bacterial infections. In this pilot study, we analyzed the [...] Read more.

Intracranial bacterial infection remains a major cause of morbidity and mortality in neurosurgical cases. Metabolomic profiling of cerebrospinal fluid (CSF) holds great promise to gain insights into the pathogenesis of central neural system (CNS) bacterial infections. In this pilot study, we analyzed the metabolites in CSF of CNS infection patients and controls in a pseudo-targeted manner, aiming at elucidating the metabolic dysregulation in response to postoperative intracranial bacterial infection of pediatric cases. Untargeted analysis uncovered 597 metabolites, and screened out 206 differential metabolites in case of infection. Targeted verification and pathway analysis filtered out the glycolysis, amino acids metabolism and purine metabolism pathways as potential pathological pathways. These perturbed pathways are involved in the infection-induced oxidative stress and immune response. Characterization of the infection-induced metabolic changes can provide robust biomarkers of CNS bacterial infection for clinical diagnosis, novel pathways for pathological investigation, and new targets for treatment. Full article

(This article belongs to the Special Issue Mass Spectrometry Analysis)

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12 pages, 2224 KiB

Open AccessArticle

Ionization of Volatile Organics and Nonvolatile Biomolecules Directly from a Titanium Slab for Mass Spectrometric Analysis

by De-Yi Huang, Meng-Jiy Wang, Jih-Jen Wu and Yu-Chie Chen

Molecules 2021, 26(22), 6760; https://doi.org/10.3390/molecules26226760 - 9 Nov 2021

Cited by 6 | Viewed by 2227

Abstract

Atmospheric pressure chemical ionization (APCI)-mass spectrometry (MS) and electrospray ionization (ESI)-MS can cover the analysis of analytes from low to high polarities. Thus, an ion source that possesses these two ionization functions is useful. Atmospheric surface-assisted ionization (ASAI), which can be used to [...] Read more.

Atmospheric pressure chemical ionization (APCI)-mass spectrometry (MS) and electrospray ionization (ESI)-MS can cover the analysis of analytes from low to high polarities. Thus, an ion source that possesses these two ionization functions is useful. Atmospheric surface-assisted ionization (ASAI), which can be used to ionize polar and nonpolar analytes in vapor, liquid, and solid forms, was demonstrated in this study. The ionization of analytes through APCI or ESI was induced from the surface of a metal substrate such as a titanium slab. ASAI is a contactless approach operated at atmospheric pressure. No electric contacts nor any voltages were required to be applied on the metal substrate during ionization. When placing samples with high vapor pressure in condensed phase underneath a titanium slab close to the inlet of the mass spectrometer, analytes can be readily ionized and detected by the mass spectrometer. Furthermore, a sample droplet (~2 μL) containing high-polarity analytes, including polar organics and biomolecules, was ionized using the titanium slab. One titanium slab is sufficient to induce the ionization of analytes occurring in front of a mass spectrometer applied with a high voltage. Moreover, this ionization method can be used to detect high volatile or polar analytes through APCI-like or ESI-like processes, respectively. Full article

(This article belongs to the Special Issue Mass Spectrometry Analysis)

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12 pages, 1767 KiB

Open AccessFeature PaperArticle

Rapid Identification between Two Fish Species Using UV-Vis Spectroscopy for Substitution Detection

by Zhaoliang Chai, Chengyu Wang and Hongyan Bi

Molecules 2021, 26(21), 6529; https://doi.org/10.3390/molecules26216529 - 28 Oct 2021

Cited by 9 | Viewed by 3081

Abstract

Fish species substitution and fraud has become a worldwide economic issue in the seafood industry. In this study, an ultraviolet-visible (UV-Vis) spectroscopy-based method was developed for the identification of fish samples. Sixty fish samples from twelve commonly consumed fish species in China were [...] Read more.

Fish species substitution and fraud has become a worldwide economic issue in the seafood industry. In this study, an ultraviolet-visible (UV-Vis) spectroscopy-based method was developed for the identification of fish samples. Sixty fish samples from twelve commonly consumed fish species in China were analyzed as models to testify the protocol. The obtained results show that UV-Vis spectroscopy combined with chemometric analysis, such as principal component analysis (PCA), can accurately distinguish two fish species by boiling fish tissue sample in trifluoroacetic acid (TFA) solution for 2 min and analyzing the resultant samples using a UV-Vis spectrometer. The developed strategy was successfully applied to the classification and identification of fish samples on the market. It is a promising strategy that can be applied to the classification and authenticity testing of closely related fish species in order to detect and recognize fish substitution. Full article

(This article belongs to the Special Issue Mass Spectrometry Analysis)

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10 pages, 2395 KiB

Open AccessArticle

Detection of Methylphenidate in Equine Hair Using Liquid Chromatography–High-Resolution Mass Spectrometry

by Benjamin C. Moeller, Luis Flores, Amel Clifford, Gwendolyne Alarcio, Mary Mosburg and Rick M. Arthur

Molecules 2021, 26(19), 5798; https://doi.org/10.3390/molecules26195798 - 24 Sep 2021

Cited by 3 | Viewed by 2375

Abstract

Methylphenidate is a powerful central nervous system stimulant with a high potential for abuse in horse racing. The detection of methylphenidate use is of interest to horse racing authorities for both prior to and during competition. The use of hair as an alternative [...] Read more.

Methylphenidate is a powerful central nervous system stimulant with a high potential for abuse in horse racing. The detection of methylphenidate use is of interest to horse racing authorities for both prior to and during competition. The use of hair as an alternative sampling matrix for equine anti-doping has increased as the number of detectable compounds has expanded. Our laboratory developed a liquid chromatography–high-resolution mass spectrometry method to detect the presence of methylphenidate in submitted samples. Briefly, hair was decontaminated, cut, and pulverized prior to liquid–liquid extraction in basic conditions before introduction to the LC-MS system. Instrumental analysis was conducted using a Thermo Q Exactive mass spectrometer using parallel reaction monitoring using a stepped collision energy to obtain sufficient product ions for qualitative identification. The method was validated and limits of quantitation, linearity, matrix effects, recovery, accuracy, and precision were determined. The method has been applied to confirm the presence of methylphenidate in official samples submitted by racing authorities. Full article

(This article belongs to the Special Issue Mass Spectrometry Analysis)

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16 pages, 2026 KiB

Open AccessArticle

Computational and Mass Spectrometry-Based Approach Identify Deleterious Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) in JMJD6

by Tianqi Gong, Lujie Yang, Fenglin Shen, Hao Chen, Ziyue Pan, Quanqing Zhang, Yan Jiang, Fan Zhong, Pengyuan Yang and Yang Zhang

Molecules 2021, 26(15), 4653; https://doi.org/10.3390/molecules26154653 - 31 Jul 2021

Cited by 2 | Viewed by 2504

Abstract

The jumonji domain-containing protein 6 (JMJD6) gene catalyzes the arginine demethylation and lysine hydroxylation of histone and a growing list of its known substrate molecules, including p53 and U2AF65, suggesting a possible role in mRNA splicing and transcription in cancer progression. Mass spectrometry-based [...] Read more.

The jumonji domain-containing protein 6 (JMJD6) gene catalyzes the arginine demethylation and lysine hydroxylation of histone and a growing list of its known substrate molecules, including p53 and U2AF65, suggesting a possible role in mRNA splicing and transcription in cancer progression. Mass spectrometry-based technology offers the opportunity to detect SNP variants accurately and effectively. In our study, we conducted a combined computational and filtration workflow to predict the nonsynonymous single nucleotide polymorphisms (nsSNPs) present in JMJD6, followed by a liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and validation. The computational approaches SIFT, PolyPhen-2, SNAP, I-Mutant 2.0, PhD-SNP, PANTHER, and SNPS&GO were integrated to screen out the predicted damaging/deleterious nsSNPs. Through the three-dimensional structure of JMJD6, H187R (rs1159480887) was selected as a candidate for validation. The validation experiments showed that the mutation of this nsSNP in JMJD6 obviously affected mRNA splicing or the transcription of downstream genes through the reduced lysyl-hydroxylase activity of its substrates, U2AF65 and p53, further indicating the accuracy of this prediction method. This research provides an effective computational workflow for researchers with an opportunity to select prominent deleterious nsSNPs and, thus, remains promising for examining the dysfunction of proteins. Full article

(This article belongs to the Special Issue Mass Spectrometry Analysis)

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15 pages, 4461 KiB

Open AccessArticle

A Multi-Omics Study of Human Testis and Epididymis

by Weimin Zheng, Yang Zhang, Chuanyu Sun, Shengyang Ge, Yifan Tan, Huali Shen and Pengyuan Yang

Molecules 2021, 26(11), 3345; https://doi.org/10.3390/molecules26113345 - 2 Jun 2021

Cited by 7 | Viewed by 3438

Abstract

The human testis and epididymis play critical roles in male fertility, including the spermatogenesis process, sperm storage, and maturation. However, the unique functions of the two organs had not been systematically studied. Herein, we provide a systematic and comprehensive multi-omics study between testis [...] Read more.

The human testis and epididymis play critical roles in male fertility, including the spermatogenesis process, sperm storage, and maturation. However, the unique functions of the two organs had not been systematically studied. Herein, we provide a systematic and comprehensive multi-omics study between testis and epididymis. RNA-Seq profiling detected and quantified 19,653 in the testis and 18,407 in the epididymis. Proteomic profiling resulted in the identification of a total of 11,024 and 10,386 proteins in the testis and epididymis, respectively, including 110 proteins that previously have been classified as MPs (missing proteins). Furthermore, Five MPs expressed in testis were validated by the MRM method. Subsequently, multi-omcis between testis and epididymis were performed, including biological functions and pathways of DEGs (Differentially Expressed Genes) in each group, revealing that those differences were related to spermatogenesis, male gamete generation, as well as reproduction. In conclusion, this study can help us find the expression regularity of missing protein and help related scientists understand the physiological functions of testis and epididymis more deeply. Full article

(This article belongs to the Special Issue Mass Spectrometry Analysis)

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15 pages, 1034 KiB

Open AccessArticle

Evaluation of Dissipation Behavior, Residues, and Dietary Risk Assessment of Fludioxonil in Cherry via QuEChERS Using HPLC-MS/MS Technique

by Shunyu Yao, Zixi Zhao, Wang Lu, Xin Dong, Jiye Hu and Xiaolu Liu

Molecules 2021, 26(11), 3344; https://doi.org/10.3390/molecules26113344 - 2 Jun 2021

Cited by 7 | Viewed by 3175

Abstract

The chemical fungicide fludioxonil is widely used to control post-harvest fungal disease in cherries. This study was implemented to investigate the dissipation behaviours and residues of fludioxonil on cherries. A reliable and efficient analytical method was established. Cherry samples from four product areas [...] Read more.

The chemical fungicide fludioxonil is widely used to control post-harvest fungal disease in cherries. This study was implemented to investigate the dissipation behaviours and residues of fludioxonil on cherries. A reliable and efficient analytical method was established. Cherry samples from four product areas were analyzed by QuEChERS and HPLC-MS/MS methods with acceptable linearity (R² > 0.99), accuracy (recoveries of 81–94%), and precision (relative standard deviation of 2.5–11.9%). The limits of quantification (LOQs) and limits of detection (LODs) of cherries were 0.01 mg/kg and 0.005 mg/kg. The dissipation of fludioxonil on cherries followed first order kinetics with half-lives of 33.7–44.7 days. The terminal residues of fludioxonil were all lower than 5.00 mg/kg, which is the MRL recommended by the European Commission. According to Chinese dietary patterns and terminal residue distributions, the risk quotient (RQs) of fludioxonil was 0.61%, revealing that the evaluated cherries exhibited an acceptably low dietary risk to consumers. Full article

(This article belongs to the Special Issue Mass Spectrometry Analysis)

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