Article
Medical Laboratory Technology
Jing Ye, Pengcheng Liu, Renming Li, Hui Liu, Wenjing Pei, Changxiu Ma, Bing Shen, Dahai Zhao, Xiaoyu Chen
Summary: This study identified differentially expressed proteins (DEPs) in connective tissue disease-associated interstitial lung disease (CTD-ILD) using label-free mass spectrometry. The results showed that these DEPs may play important roles in the development of CTD-ILD and can be potential new biomarkers for early diagnosis of CTD-ILD.
JOURNAL OF CLINICAL LABORATORY ANALYSIS
(2022)
Article
Agronomy
Archis Pandya, Bjorn Thiele, Andres Zurita-Silva, Bjorn Usadel, Fabio Fiorani
Summary: The study evaluated saponin content and their corresponding sapogenins in 114 different quinoa accessions, showing considerable variability in saponin content in quinoa. Approximately 75% of the genotypes were classified as low-saponin content lines, which is promising for current and future quinoa breeding programs. Additionally, twelve saponins of the oleanane type were identified, including a previously unreported compound, contributing to the valorization of genetic resources for quinoa.
Article
Biochemical Research Methods
Jianbo Fu, Qingxia Yang, Yongchao Luo, Song Zhang, Jing Tang, Ying Zhang, Hongning Zhang, Hanxiang Xu, Feng Zhu
Summary: Label-free quantification (LFQ) is an important technique in proteomics due to its broad proteome coverage and enhanced reproducibility. In this study, an R package EVALFQ was developed to evaluate and discover well-performing LFQ chains from over 3000 options.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Jianbo Fu, Qingxia Yang, Yongchao Luo, Song Zhang, Jing Tang, Ying Zhang, Hongning Zhang, Hanxiang Xu, Feng Zhu
Summary: The label-free quantification (LFQ) is a powerful technique in proteomics due to its broad proteome coverage, great dynamic ranges, and enhanced analytical reproducibility. However, determining the well-performing LFQ chain is challenging due to the dependence on data and the diverse possibilities. In this study, a unique R package EVALFQ was developed for performance evaluation of >3000 LFQ chains, utilizing multiple criteria, spiking proteins, and comprehensive assessment. This package is expected to attract broad interests in the field of proteomic quantification.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Huu-Quang Nguyen, Dabin Lee, Yeoseon Kim, Geul Bang, Kun Cho, Young-Sun Lee, Jong Eun Yeon, David M. Lubman, Jeongkwon Kim
Summary: This study utilized LC-MS/MS to analyze the protein expression profiles of extracellular vesicles from serum samples of patients with various fatty liver diseases, revealing significant differences in protein expression levels of apolipoproteins, immunoglobulins, and other markers. Through principal component analysis, a clear differentiation between ALD and NAFLD was achieved. The up-regulation of alpha-2-macroglobulin in alcoholic hepatitis and apolipoprotein C3 in NAFLD were identified as significant findings.
JOURNAL OF PROTEOMICS
(2021)
Article
Plant Sciences
Muhammad Afzal, Malte Sielaff, Valentina Curella, Manjusha Neerukonda, Khaoula El Hassouni, Detlef Schuppan, Stefan Tenzer, C. Friedrich H. Longin
Summary: The study analyzed the expression of 756 proteins across 150 wheat cultivars using proteomics and found that environmental conditions have a significant impact on protein expression. Wheat cultivars varied greatly in their protein profiles, with 114 proteins being crucial for bread quality and human health.
Article
Biochemistry & Molecular Biology
Delphine Vincent, AnhDuyen Bui, Doris Ram, Vilnis Ezernieks, Frank Bedon, Joe Panozzo, Pankaj Maharjan, Simone Rochfort, Hans Daetwyler, Matthew Hayden
Summary: This study optimized a LC-MS shotgun quantitative proteomics method to screen wheat genotypes for breeding lines with better performance. A large number of wheat proteins were identified using this method, and data mining tools were used to explore the flour proteome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Xuan Guo, Lei Zhang, Zihan Lei, Zhe Hou, Hui Li, Xiaodong Li, Jing Dong, Ling Song, Dingding Chen, Dongyang Liu
Summary: The objective of this study was to develop a LC-MS/MS method for quantitation of seven cytochrome P450 (CYP450) enzymes. The method was validated for selectivity, linearity, stability, accuracy, and precision. The abundance of the enzymes in human liver microsomes and CYP3A4 in placenta was accurately determined using this method.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2023)
Article
Chemistry, Applied
Sridevi Muralidharan, Yan Yee Poon, Graeme C. Wright, Paul A. Haynes, Nanju A. Lee
Summary: This study used mass spectrometry-based proteomic analysis on Australian peanut recombinant inbred lines and found significant protein expression differences between high and low polyphenol expressing RILs. Metabolic changes, including increased enzymatic breakdown of sugars and phenylalanine biosynthesis, were observed in polyphenol-rich RILs. The study also revealed overexpression of phenylpropanoid pathway and antioxidant enzymes, such as catalase, in the polyphenol-rich peanut phenotype.
Article
Agriculture, Multidisciplinary
Barbara Prandi, Chiara Vacca, Stefano Sforza, Tullia Tedeschi
Summary: The increasing awareness of consumers on sustainable food chains has caused a shift in consumption from animal protein sources to plant protein sources. Soy, which is both relevant for human food use and animal feed, has a high protein content but is accompanied by antinutritional factors such as Kunitz's trypsin inhibitor (KTI). A direct label-free liquid chromatography-mass spectrometry (LC-MS) method has been developed to identify and quantify Kunitz inhibitor KTI3 in soybean and its derivative products, using a marker peptide specific to the protein of interest. The results of the LC-MS method were compared with spectrophotometric trypsin inhibition, demonstrating the complementarity of these two types of analysis.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Agriculture, Dairy & Animal Science
Alessio Di Luca, Francesca Bennato, Andrea Ianni, Lisa Grotta, Michael Henry, Paula Meleady, Giuseppe Martino
Summary: In this study, proteomic technologies were used to compare the milk proteome of two goat breeds, Teramana and Saanen. The analysis identified 29 proteins that could discriminate between the two breeds. This research contributes to our understanding of the goat milk proteome and provides important information for future studies on goat milk proteins.
Article
Biochemical Research Methods
Robert Winkler
Summary: Comparing multiple label-free shotgun proteomics datasets requires various data processing steps, including peptide-spectrum matching, protein inference, and quantification. ProtyQuant is a tool that integrates data from multiple experiments, aiding in protein comparison and providing intuitive information on protein probability and quantity. The accumulated peptide probability (app) serves as a reliable measure of 'Protein Presence,' facilitating protein identification and quantification in comparative proteomics.
JOURNAL OF PROTEOMICS
(2021)
Article
Biochemical Research Methods
Rongmei Huang, Yi Hong, Yike Wu, Weifeng Li, Wenlan Liu
Summary: We developed a new LC-MS/MS method for simultaneous determination of serum testosterone and free testosterone levels. The method is simple to perform and can be applied in clinical practice, providing important information for diagnosis, treatment, and monitoring of androgen-related diseases.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Plant Sciences
Zhi-Jun Shen, Su-Xia Xu, Qing-Yun Huang, Zi-Yang Li, Yi-Ding Xu, Chun-Song Lin, Yi-Jin Huang
Summary: This study investigated the mechanism of seed maturation in quinoa through morphological characteristics and TMT proteomics analysis. The accumulation and pathways of proteins during maturation conversion were found to change, and changes in morphological characteristics related to maturation were also discovered. These findings contribute to the genetic improvement of quinoa.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Aleksandra E. Lewandowska, Anna Fel, Marcel Thiel, Paulina Czaplewska, Krzysztof Lukaszuk, Jacek R. Wisniewski, Stanislaw Oldziej
Summary: Two label-free quantitative workflows based on different high-resolution mass spectrometers and LC setups were presented for the analysis of human follicular fluid proteome, with around 1000 proteins identified in each workflow. The concentration values obtained from both workflows showed significant correlation, leading to unified lists of proteins linked to oocyte maturity and blastocyst development. The Quad-Orbitrap workflow is suitable for in-depth analysis of low abundant proteome without extensive fractionation, while the Triple Quad-TOF workflow offers a more robust approach with potential for effectiveness with increasing number of analyzed samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Zoran Minic, Nico Huettmann, Suttinee Poolsup, Yingxi Li, Vanessa Susevski, Emil Zaripov, Maxim V. Berezovski
Summary: In this study, the phosphoproteomic analysis of breast cancer-derived small extracellular vesicles (sEVs) provided insights into the molecular and cellular regulatory mechanisms important for breast cancer tumor progression and metastasis. Functional metabolic enzymes were found in sEVs, which could potentially be used for early breast cancer diagnosis and therapy.
Article
Biology
Abdolamir Allameh, Nico Huettmann, Edouard Charlebois, Angeliki Katsarou, Wen Gu, Konstantinos Gkouvatsos, Elisa Pasini, Mamatha Bhat, Zoran Minic, Maxim Berezovski, Maria Guido, Carine Fillebeen, Kostas Pantopoulos
Summary: HJV has a hepatoprotective function and its deficiency in mice leads to mitochondrial dysfunction and hepatocarcinogenesis.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Applied
Rocio Galindo-Lujan, Laura Pont, Victoria Sanz-Nebot, Fernando Benavente
Summary: This study presents a method using mass spectrometry to analyze quinoa proteins, allowing for accurate identification of different commercial quinoa varieties. The developed method provides reliable protein fingerprints for classification of quinoa products based on their protein profiles.
Article
Food Science & Technology
Rocio Galindo-Lujan, Laura Pont, Victoria Sanz-Nebot, Fernando Benavente
Summary: A label-free mass spectrometry-based shotgun proteomics analysis was used to identify quinoa grain proteins with potential immunonutritional bioactivities, including those related to cancer. The study also compared the proteome similarities and differences of different types of quinoa grains. This research provides a basis for future exploration of the bioactivity and immunonutrition of quinoa proteins.
Article
Chemistry, Analytical
Hiba Salim, Laura Pont, Estela Gimenez, Fernando Benavente
Summary: This study presents an online aptamer affinity solid-phase extraction direct mass spectrometry (AA-SPE-MS) method for the rapid purification, preconcentration, and characterization of alpha-synuclein (alpha-syn), a protein biomarker related to Parkinson's disease. The method utilizes SPE microcartridges and replaces the separation voltage with a pressure of 100 mbar to elute the protein towards the mass spectrometer. The developed method shows good repeatability, satisfactory linearity, and lower limits of detection compared to other techniques.
ANALYTICA CHIMICA ACTA
(2023)
Article
Food Science & Technology
Rana M. Ibrahim, Basma M. Eltanany, Laura Pont, Fernando Benavente, Shahira A. ElBanna, Asmaa M. Otify
Summary: Plant extracts are being studied as alternative antimicrobial agents for multidrug-resistant bacteria. In this study, the metabolic profiles of red and green leaves of two Brassica juncea varieties were evaluated using liquid chromatography-quadrupole time-of-flight tandem mass spectrometry, molecular networking, and chemometrics. The extracts showed significant antibacterial activity against Staphylococcus aureus and Enterococcus faecalis, and the chemical compounds positively correlated to bioactivity were identified.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Food Science & Technology
Asmaa M. Otify, Shahira A. ElBanna, Basma M. Eltanany, Laura Pont, Fernando Benavente, Rana M. Ibrahim
Summary: This study characterized the metabolite profiles of six lettuce varieties and established their correlation with antivirulence effects. Various metabolites were identified, and red varieties showed higher levels of chlorogenic and chicoric acids indicating antioxidant properties. Romaine longifolia exhibited enrichment in amino acids and disaccharides, while crispa, capitata, and lolla bionda had a high content of β-carboline alkaloids. All varieties demonstrated antibacterial potential against Staphylococcus aureus strains, and specific bioactives such as sesquiterpenes, β-carboline alkaloids, amino acids, and oxy-fatty acids were identified. The results highlight the significance of lettuce as a functional food source and suggest breeding programs should focus on varieties rich in antibacterial agents.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Biochemical Research Methods
Montserrat Mancera-Arteu, Fernando Benavente, Victoria Sanz-Nebot, Estela Gimenez
Summary: In this study, different chromatographic sorbents were evaluated for the analysis of glycopeptides. The PBA sorbent showed the most promising results, leading to the development of a selective and sensitive preconcentration method for glycopeptides. The method was successfully applied to the analysis of recombinant human erythropoietin (rhEPO) and demonstrated improved results compared to previous methods.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Analytical
Maria Vergara-Barberan, Monica Catala-Icardo, Ernesto F. Simo-Alfonso, Fernando Benavente, Jose Manuel Herrero-Martinez
Summary: This study describes the development of an aptamer-functionalized stir bar sorptive extraction (SBSE) coating for selective isolation and preconcentration of an allergenic food protein, concavanalin A (Con A), followed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF-MS) determination. The aptamer-functionalized stir bar exhibited high selectivity for Con A and was successfully applied to the determination of Con A in various food matrices. The developed method showed good recoveries and stability, indicating its potential for the extraction of proteins and peptides from complex samples.
Article
Medicine, Research & Experimental
Suttinee Poolsup, Emil Zaripov, Nico Huttmann, Zoran Minic, Polina V. Artyushenko, Irina A. Shchugoreva, Felix N. Tomilin, Anna S. Kichkailo, Maxim V. Berezovski
Summary: This study aimed to develop a label-free optical aptasensor using a novel single-stranded DNA aptamer to detect the SARS-CoV-2 nucleocapsid (N) protein. The tNSP3 aptamer was identified to bind the N protein of different variants with high affinity. Utilizing tNSP3, the N protein could be detected in human saliva with a limit of detection of 4.5 nM. Mass spectrometry analysis and molecular dynamics simulation provided insights into the binding mechanism of tNSP3 with the N protein. Overall, this aptamer demonstrated potential as an analytical tool for COVID-19 diagnosis.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Chemistry, Analytical
Laila Bchara, Ramon Eritja, Raimundo Gargallo, Fernando Benavente
Summary: A capillary electrophoresis method with UV detection has been developed for analyzing the folding equilibrium of i-motif DNA. Multivariate curve resolution-alternating least-squares (MCR-ALS) has been used to separate folded and unfolded species and estimate melting temperatures (Tm).
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Maria Vergara-Barberan, Ernesto Francisco Simo-Alfonso, Jose Manuel Herrero-Martinez, Fernando Benavente
Summary: An aptamer affinity sorbent was developed for clean-up, preconcentration, separation, and characterization of a food allergen protein. The sorbent, based on magnetic bead particles modified with an aptamer against the target protein concanavalin A, was packed in SPE microcartridges. The developed method showed good linearity, with a low limit of detection, satisfactory repeatability, and the ability to reuse the microcartridges.
MICROCHEMICAL JOURNAL
(2023)
Article
Chemistry, Applied
M. Graca Dias, Elsa Vasco, Francisco Ravasco, Lufsa Oliveira
Summary: This study estimated the vitamin D intake of "adults" and "elderly" populations in Portugal using the TDS methodology. The results showed that the majority of people had inadequate vitamin D intake, well below the Dietary Reference Values.
Article
Chemistry, Applied
Yanan Wang, Jiachen Shi, Yong-Jiang Xu, Chin-Ping Tan, Yuanfa Liu
Summary: This study investigates the variations in lipid digestion profiles among individuals of different ages using in vitro digestion models. The findings suggest that adults have a more comprehensive lipid digestion compared to infants, and infants tend to release shorter chain length and more saturated free fatty acids during digestion. Additionally, the particle sizes in the stomach of the elderly were consistently larger. This study enhances our understanding of how lipids with different degrees of unsaturation undergo digestion in diverse age groups.
Article
Chemistry, Applied
Hyunjong Yu, Huisu Kim, Pahn-Shick Chang
Summary: Chitosan-pectin emulsion-filled hydrogel (EFH) was developed to enhance the bioaccessibility of lipophilic bioactive compounds through intestinal delivery. The EFH, prepared without crosslinking agents, demonstrated improved mechanical strength and compactness with higher pectin concentration. It retained the emulsion at pH 2.0 and released it at pH 7.4, resulting in enhanced release of free fatty acids and improved bioaccessibility of curcumin.
Article
Chemistry, Applied
Tongze Zhang, Siqi Hong, Jia-Rong Zhang, Pin-He Liu, Siyi Li, Zixian Wen, Jianwei Xiao, Guirong Zhang, Olivier Habimana, Nagendra P. Shah, Zhongquan Sui, Harold Corke
Summary: Lactic acid fermentation significantly affects the morphology and physicochemical properties of proso millet starch, including the formation of surface indentations and small pores, decrease in gelatinization temperatures, and changes in hardness and adhesiveness.
Article
Chemistry, Applied
Liqin Kong, Feng Hong, Peng Luan, Yiping Chen, Yaoze Feng, Ming Zhu
Summary: This study presents a novel impedance biosensor using composite nanomaterials and T1R1 as a signal probe, which can competitively and ultra-sensitively detect umami intensity. The biosensor exhibits exceptional analytical performance and is suitable for food flavor evaluation.
Article
Chemistry, Applied
Kunying Lv, Yixin Yang, Qilong Li, Ran Chen, Liang Deng, Yiwei Zhang, Ning Jiang
Summary: Horse's milk, with its high nutritional value and low allergenic proteins, could be a substitute for cow's milk in infant consumption. A proteomic method was used to identify and compare milk fat globule membrane (MFGM) and whey proteins from different horse breeds. The study found differences in protein composition and functionality, which could support the development of formulas more suitable for human infants.
Article
Chemistry, Applied
Enrique Jacobo Diaz-Montana, Helene Brignot, Ramon Aparicio-Ruiz, Thierry Thomas- Danguin, Maria Teresa Morales
Summary: Sensory perception of virgin olive oil is influenced by phenols and volatiles, which are affected by the composition of the oil and biological factors. This study investigated the effect of saliva and phenols on the release of volatiles, and found that the presence of phenols decreased the release of saturated volatiles.
Article
Chemistry, Applied
Wei Zhou, Rui Zhang, Zhen Cai, Fangfang Wu, Yong Hu, Chao Huang, Kun Hu, Yun Chen
Summary: Environmentally friendly and outstanding pH-responsive cationic starch nanoparticles (CSNP) were prepared from pH-sensitive starch. CSNP exhibited nanosize and regular sphere, highly free-flowing molecular chains, and demonstrated excellent pH responsiveness through multiple emulsion/demulsification transitions.
Article
Chemistry, Applied
Andrea Koo, Vinayak Ghate, Weibiao Zhou
Summary: This study suggests that direct seeding may negatively affect the nutritional quality of crops, causing a decrease in ascorbic acid, vitamin K, and total glucosinolate content.
Article
Chemistry, Applied
Tonghao Du, Yazhou Xu, Xiaoyan Xu, Shijin Xiong, Linli Zhang, Biao Dong, Jinqing Huang, Tao Huang, Muyan Xiao, Tao Xiong, Mingyong Xie
Summary: This study successfully improved the ACE inhibitory activity of black sesame seeds by fermenting them with Lactobacillus Plantarum NCU116 and hydrolyzing them using acid protease. The RF-PSO model was used to predict the ACE inhibitory activity during the hydrolysis process. Eight peptides with ACE inhibitory activity were identified from fermented black sesame seed hydrolysates after separation and screening.
Article
Chemistry, Applied
Yao Liu, Songyi Lin, Kexin Liu, Shan Wang, Qiaozhen Liu, Na Sun
Summary: This study analyzed the structural changes of shrimp proteins during digestion, predicted the immunodominant epitopes, and validated their allergenicity. The results showed that shrimp proteins were degraded into peptides during digestion, but still carried IgE epitopes that trigger allergic reactions.
Article
Chemistry, Applied
Tiantian Fu, Hongwei Cao, Yu Zhang, Xiao Guan
Summary: This study investigates the impact of milling on the active components in rice, with a focus on the stability and bioaccessibility of phenols, VB1, and alpha-GABA during cooking and digestion. The findings show that milling exacerbates the instability of gamma-GABA during cooking and VB1 during digestion, and it affects the bioaccessibility of these active compounds.
Article
Chemistry, Applied
Zhihao Yang, Yanru Hou, Min Zhang, Puxin Hou, Chang Liu, Lu Dou, Xiaoyu Chen, Lihua Zhao, Lin Su, Ye Jin
Summary: This study investigated the molecular mechanism of feeding regimes on lamb flavor by using TMT labeling combined with MS. The results showed that pasture-fed groups had higher levels of amino acids and volatile flavor substances compared to concentrate-fed groups. Additionally, several differentially abundant proteins associated with lamb flavor were identified.
Article
Chemistry, Applied
Zixuan Xie, De Zhang, Junyu Zhu, Qianqian Luo, Jun Liu, Jingtao Zhou, Xiaoyong Wang, Yuqiong Chen, Zhi Yu, Dejiang Ni
Summary: This study investigated the acidification of aroma-enhanced black tea during storage. Analysis of non-volatile substances and organic acids using UPLC-Q-TOF/MS and HPLC revealed a decrease in soluble sugars and amino acids, while an increase in organic acids such as oxalic acid, malic acid, and quinic acid. In vitro experiments further demonstrated that the acidification is a result of the decomposition of sugars and amino acids by heating, as well as the oxidation of aromatic aldehydes. Additionally, the study showed that the taste composition of tea infusion is altered, with reduced amino acids, catechins, soluble sugars, and flavonoids. This research provides a theoretical basis for improving the quality of black tea.
Article
Chemistry, Applied
Lin Wang, Falai Ma, Zihan Li, Yan Zhang
Summary: This study developed time-temperature integrators based on amyloglucosidase@Cu3(PO4)2 nanoflowers for monitoring the freshness of chilled pork. The results showed that the integrators were highly reliable and accurate in predicting the quality of chilled pork.
