Article
Biochemical Research Methods
Sujun Li, Jianhui Zhu, David M. Lubman, He Zhou, Haixu Tang
Summary: Liquid chromatography coupled with tandem mass spectrometry is commonly used in large-scale glycoproteomic studies. A novel concurrent approach for glycopeptide identification in multiple related data sets is presented using spectral clustering and spectral library searching. Evaluation on two large-scale data sets showed that this approach can identify 105%-224% more spectra as glycopeptides compared to using Byonic alone, enabling the discovery of potential biomarkers in hepatocellular carcinoma.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Fayaj A. Mulani, Sharvani S. Nandikol, Jagadeesh S. Kajjihundi, Niranjana Pathappa, Sharanappa Puttappa, Hirekodathakallu Thulasiram
Summary: Meliaceae plants are widely used in agriculture, folklore, and traditional medicine, and contain diverse limonoids with various bioactivities. Accurate detection of these compounds from plant tissue extracts or biological samples is challenging. In this study, a new method was developed for the identification, quantification, and characterization of limonoids in different plant tissue extracts using minimal plant material.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Hassan Shikshaky, Eman Abdelnaby Ahmed, Ali Mostafa Anwar, Aya Osama, Shahd Ezzeldin, Antony Nasr, Sebaey Mahgoub, Sameh Magdeldin
Summary: This article aims to develop a novel SWATH platform for metabolite identification using accurate mass spectral library, providing new avenues for clinical diagnosis, molecular medicine, and therapeutic drug monitoring and development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Eunjung Kim, Sihyun Park, Hyunjin Park, Jangduck Choi, Hae Jung Yoon, Jeong-Han Kim
Summary: The study aimed to develop a comprehensive and simple method for the simultaneous determination of anthelmintic and antiprotozoal drug residues in fish. The QuEChERS method was used for sample preparation, followed by LC-MS/MS analysis, resulting in high accuracy and recovery rates.
Article
Engineering, Environmental
Zhengzhi Xie, Jin Y. Chen, Hong Gao, Rachel J. Keith, Aruni Bhatnagar, Pawel Lorkiewicz, Sanjay Srivastava
Summary: We developed an exposomics platform to analyze urinary mercapturic acid metabolites from reactive chemicals. Our workflow enabled profiling of known and unreported MAs from endogenous and environmental sources, and revealed increased levels of several MAs in smokers. This method has wide applications in exposure-wide association studies.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Environmental Sciences
Vincent Dufour, Laure Wiest, Sylvain Slaby, Francois Le Cor, Lucile Auger, Olivier Cardoso, Laurence Curtet, Laure Pasquini, Xavier Dauchy, Emmanuelle Vulliet, Damien Banas
Summary: Monitoring pesticides in small organisms in the environment requires sensitive analytical methods. This study developed a miniaturized extraction protocol for small biotic samples, allowing for the characterization of multiple pesticides and transformation products. The method showed high extraction rates and recoveries, making it an effective tool for analyzing polar pesticides in small organisms.
Article
Biochemical Research Methods
Prasad Phapale, Andrew Palmer, Rose Muthoni Gathungu, Dipali Kale, Britta Brugger, Theodore Alexandrov
Summary: EMBL-MCF is an open LC-MS/MS spectral library with over 1600 fragmentation spectra from 435 authentic standards of endogenous metabolites and lipids. It features chromatographic profiles acquired with different LC-MS methods and coverage of different adduct ions. The library contains many biologically important metabolites and unique metabolites and lipids compared to other public libraries.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Clinical Neurology
Stefania Mondello, Firas H. Kobeissy, Yehia Mechref, Jingfu Zhao, Samer El Hayek, Kazem Zibara, Monica Moresco, Giuseppe Plazzi, Filomena I. I. Cosentino, Raffaele Ferri
Summary: Comparative proteomic analysis of blood samples from patients with RLS and healthy individuals identified multiple proteins associated with RLS, highlighting the multifactorial nature of the disease. The study also revealed a set of circulating proteins that may have clinical importance as biomarkers and therapeutic targets for RLS.
NATURE AND SCIENCE OF SLEEP
(2021)
Article
Chemistry, Analytical
Alexander Kasperkiewicz, Sofia Lendor, Janusz Pawliszyn
Summary: The study investigated the relative matrix effects between coated blade spray (CBS) and liquid chromatographic separation approaches in multiresidue pesticide analysis in strawberry samples. The findings showed that acceptable slope relative standard deviations were observed under both CBS-MS/MS and LC-MS/MS approaches, indicating the elimination of relative matrix effects and no compromise with matrix effects when using the direct-to-MS approach. Additionally, the resistance of the methods to excipients present in pesticide formulations was highlighted.
Article
Pharmacology & Pharmacy
Xiqing Bian, Yida Zhang, Na Li, Menglin Shi, Xiaolin Chen, Hui-Lu Zhang, Jie Liu, Jian-Lin Wu
Summary: Trace amines (TAs) are metabolically related to catecholamine and associated with cancer and neurological disorders. A sensitive method using diisopropyl phosphite coupled with chip two-dimensional liquid chromatography tandem triple-quadrupole mass spectrometry (LC-QQQ/MS) was developed to simultaneously determine TAs and associated metabolites. The results showed significantly altered TAs and associated metabolites in hepatoma cells after sorafenib treatment, indicating the potential for elucidating disease mechanisms and diagnosing diseases based on the physiological functions of TAs.
JOURNAL OF PHARMACEUTICAL ANALYSIS
(2023)
Article
Engineering, Environmental
Chihiro Gau, Satoshi Sato, Daizhou Zhang, Yasuhiro Ishibashi, Jun Kobayashi
Summary: This study investigated the rejection of trace organic compounds and the recovery of nutrients in human urine using a seawater-driven FO-MD hybrid system. The results showed high rejection and recovery efficiencies, unaffected by the draw solution temperature.
WATER SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Marina A. Dikunets, Grigory A. Dudko, Edward D. Virus
Summary: The association between adrenocortical steroidogenesis and high intensity exercise in elite athletes is understudied due to the wide range of steroid concentrations in serum and limitations in sampling professional athletes. To overcome this challenge, a novel approach using LC-MS/MS and dual-polarity electrospray ionization was developed and validated for targeted serum metabolic profiling. This method allows for the quantitative determination of 14 stress resistance biomarkers within 8.5 minutes using a small amount of specimen.
Article
Multidisciplinary Sciences
Tzu-Yun Kuo, Jen-Hung Wang, Yung-Wen Huang, Ting-Yi Sung, Ching-Tai Chen
Summary: In this study, a novel quantitation pipeline that combines sequence database searching, spectral library searching, and a feature-based peptide-spectrum-match (PSM) filter is proposed to improve the quantitation accuracy of isobaric labeling-based mass spectrometry. The results demonstrate that this pipeline can enhance the overall quantitation accuracy at both the PSM and protein levels. This is the first study to utilize spectral library searching to improve isobaric labeling-based quantitation.
SCIENTIFIC REPORTS
(2023)
Article
Environmental Sciences
Jianmin Zou, Bo Yao, Shuwen Yan, Weihua Song
Summary: A novel mixed-mode online solid-phase extraction (SPE) method was developed in this study for the recovery of trace organic contaminants (TrOCs) from environmental water samples. The method was further coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) to establish a fully automated analytic method. The performance of the mixed-mode SPE cartridge was evaluated and the method was successfully applied for the screening and quantification of TrOCs in various water matrices.
ENVIRONMENTAL POLLUTION
(2022)
Article
Chemistry, Applied
Jing Zhang, Ya Xu, Chi-Tang Ho, Jia-Qi Qiu, Xiao-Hui Qiu, Zhi-Hai Huang, Liang Zhang, Wen Xu
Summary: This study comprehensively characterized the components of Medog lemon, a wild citron species native to southeastern Tibet, using advanced analytical techniques. The analysis identified numerous new phytochemicals in Medog lemon and revealed its distinct chemical composition compared to cultivated citron and fingered citron. The unique morphological and chemical characteristics, along with its strong antioxidant properties, suggest that Medog lemon could potentially serve as a beneficial new food resource for human health.
Article
Food Science & Technology
Xiaomin Zhou, Maria M. Ulaszewska, Cristian De Gobba, Ansmund Rinnan, Malene W. Poulsen, Jie Chen, Fulvio Mattivi, Rikke Vingborg Hedegaard, Leif Horsfelt Skibsted, Lars Ove Dragsted
Summary: This study identified potential metabolites as biomarkers of intake of heat-treated skimmed milk powder (HSMP) through a parallel study with rats, suggesting the effects of HSMP consumption or dietary AGEs on human health.
MOLECULAR NUTRITION & FOOD RESEARCH
(2021)
Article
Chemistry, Analytical
Jonatan Dias, Sonia Herrera Lopez, Hans Mol, Andre de Kok
Summary: Hydrophilic interaction liquid chromatography is recognized as an important solution for separating polar compounds not amenable to reverse phase chromatography. This study evaluated three different hydrophilic liquid chromatography stationary phases for the determination of 14 highly polar anionic molecules, showcasing different matrix effects and interactions between compounds. The use of isotopically labeled internal standards enabled acceptable quantitative performance and identification down to 0.02mgkg(-1) for most compounds.
JOURNAL OF SEPARATION SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Lapo Renai, Cristina Vanessa Agata Scordo, Ugo Chiuminatto, Marynka Ulaszewska, Edgardo Giordani, William Antonio Petrucci, Francesca Tozzi, Stefania Nin, Massimo Del Bubba
Summary: This study provided a detailed analysis of antioxidant and bioactive compounds in different varieties of Rubus idaeus L. fruits, compared to Rubus occidentalis L. black raspberry. Certain unique compounds were identified for the first time in raspberry fruits, and differences in metabolic traits were observed between different raspberry varieties.
Article
Chemistry, Applied
Dorrain Yanwen Low, Pierre Micheau, Ville Mikael Koistinen, Kati Hanhineva, Laszlo Abranko, Ana Rodriguez-Mateos, Andreia Bento da Silva, Christof van Poucke, Conceicao Almeida, Cristina Andres-Lacueva, Dilip K. Rai, Esra Capanoglu, Francisco A. Tomas Barberan, Fulvio Mattivi, Gesine Schmidt, Gozde Gurdeniz, Katerina Valentov, Letizia Bresciani, Lucie Petraskova, Lars Ove Dragsted, Mark Philo, Marynka Ulaszewska, Pedro Mena, Raul Gonzalez-Dominguez, Rocio Garcia-Villalba, Senem Kamiloglu, Sonia de Pascual-Teresa, Stephanie Durand, Wieslaw Wiczkowski, Maria Rosario Bronze, Jan Stanstrup, Claudine Manach
Summary: The study tested the performance of PredRet in predicting retention times for plant food bioactive metabolites and demonstrated high prediction accuracy in an external validation test. Retention time prediction depends on the shape and type of LC gradient, as well as the number of commonly measured compounds.
Article
Biochemical Research Methods
Lapo Renai, Claudia Ancillotti, Marynka Ulaszewska, Mar Garcia-Aloy, Fulvio Mattivi, Riccardo Bartoletti, Massimo Del Bubba
Summary: This study presents different chemometric selection workflows for the discovery of potential exposure markers (PEMs) in untargeted LC-HRMS metabolomics, aiming to identify statistically significant PEMs using multivariate or univariate parametric or non-parametric data analysis methods. The study successfully identified a restricted group of significant features and annotated several metabolites associated with nutrition intake. Additionally, the analysis of longitudinal data revealed significant PEMs that can discriminate between different interventions.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Letter
Oncology
Concetta Panebianco, Federica Pisati, Maria Ulaszewska, Annapaola Andolfo, Annacandida Villani, Federica Federici, Manna Laura, Eleonora Rizzi, Adele Potenza, Tiziana Pia Latiano, Francesco Perri, Claudio Tripodo, Valerio Pazienza
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Amaia Lejarazu-Larranaga, Juan M. Ortiz, Serena Molina, Sylwin Pawlowski, Claudia F. Galinha, Vanessa Otero, Eloy Garcia-Calvo, Svetlozar Velizarov, Joao G. Crespo
Summary: This work explores the application of reverse osmosis upcycled membranes in Donnan Dialysis and ion exchange membrane bioreactor processes for nitrate removal from water. Spectroscopy techniques were used to evaluate the performance and changes of the membranes, and the technical feasibility of using upcycled AEMs was validated. This membrane recycling concept can also be applied for the removal and recovery of other target negatively charged species.
Article
Biochemistry & Molecular Biology
Laura Rodriguez-Saez, Sotiris I. Patsios, Jorge Senan-Salinas, Junkal Landaburu-Aguirre, Serena Molina, Eloy Garcia-Calvo
Summary: This study explores the feasibility of using recycled ultrafiltration membranes as submerged flat-sheet membranes in an aerobic membrane bioreactor for the first time. The results show that the recycled ultrafiltration membranes perform similarly to commercial membranes in terms of rejection performance, fouling behavior, and permeate quality. The recycled membranes exhibit higher fouling resistance and have the potential to be competitively used in industrial applications, as indicated by a preliminary economic assessment.
Article
Nutrition & Dietetics
Francesca Fava, Maria M. Ulaszewska, Matthias Scholz, Jan Stanstrup, Lorenzo Nissen, Fulvio Mattivi, Joan Vermeiren, Douwina Bosscher, Carlo Pedrolli, Kieran M. Tuohy
Summary: This study aimed to evaluate the effects of wheat aleurone supplemented foods on human health. The results showed that aleurone has the potential to modulate gut microbial metabolic output and increase the abundance of bifidobacteria in feces. However, it did not have a significant impact on plasma homocysteine or other cardiovascular disease biomarkers.
EUROPEAN JOURNAL OF NUTRITION
(2022)
Article
Engineering, Environmental
Jorge Senan-Salinas, Junkal Landaburu-Aguirre, Jorge Contreras-Martinez, Eloy Garcia-Calvo
Summary: Recycling end-of-life RO membrane modules into FO membranes is an innovative approach to integrate membrane science into Circular Economy. This study assessed the environmental potential of this strategy and compared it with commercial TFC and CTA membranes. The results showed the interest in most impact categories and identified solvent losses as a source of error.
RESOURCES CONSERVATION AND RECYCLING
(2022)
Article
Medicine, Research & Experimental
Concetta Panebianco, Annacandida Villani, Federica Pisati, Fabrizio Orsenigo, Marynka Ulaszewska, Tiziana Pia Latiano, Adele Potenza, Annapaola Andolfo, Fulvia Terracciano, Claudio Tripodo, Francesco Perri, Valerio Pazienza
Summary: This study demonstrates the potential role of butyrate in the treatment of pancreatic cancer, showing that it can enhance the effectiveness of chemotherapy while reducing associated damages, as well as improving liver and kidney function.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Biochemistry & Molecular Biology
Anamary Pompa-Pernia, Serena Molina, Amaia Lejarazu-Larranaga, Junkal Landaburu-Aguirre, Eloy Garcia-Calvo
Summary: This study validated the application capability of recycled nanofiltration (rNF) membranes and recycled anion-exchange membranes (rAEMs) obtained from end-of-life reverse osmosis (RO) membranes in saline wastewater treatment. Recycled membranes provide a cost-effective and environmentally friendly option by integrating membrane-based technology into a circular economy model. The results showed that rNF membranes exhibited high selective rejection of divalent ions, while rAEMs demonstrated appropriate demineralization rate in comparison to commercial membranes without compromising power consumption.
Article
Biochemistry & Molecular Biology
Jose Fernando Rinaldi de Alvarenga, Mar Garcia-Aloy, Marynka Ulaszewska, Sebastian Zagmutt, Marta Perez-Montero, Urska Vrhovsek, Rosa M. Lamuela-Raventos, Rosalia Rodriguez-Rodriguez
Summary: This study investigates the impact of sofrito, a tomato and olive oil-based sauce, on energy metabolism in obese rats. The results show that sofrito intake promotes lipid oxidation, ketogenesis activation, and alters the lipidomic profile in fat depots. These findings provide further evidence for the beneficial effects of sofrito and components of the Mediterranean diet against obesity.
Article
Biochemistry & Molecular Biology
Lapo Renai, Marynka Ulaszewska, Fulvio Mattivi, Riccardo Bartoletti, Massimo Del Bubba, Justin J. J. van der Hooft
Summary: This study investigates the annotation and discovery capabilities of the Feature-Based Molecular Networking (FBMN) approach in untargeted metabolomics by adding two nutritionally-relevant mass spectral libraries. The results show that the combination of FBMN approach with these additional libraries achieves a structural annotation coverage comparable to or higher than existing non-commercial annotation workflows. Furthermore, the postprandial behavior of annotated metabolites can be analyzed using a simple chemometric tool.
Article
Biochemistry & Molecular Biology
Jorge Senan-Salinas, Junkal Landaburu-Aguirre, Raquel Garcia-Pacheco, Eloy Garcia-Calvo
Summary: This study conducted an environmental analysis of the entire life cycle of recycled nanofiltration (r-NF) membranes for the first time, emphasizing the importance of energy use during the usage stage. By evaluating different strategies and energy sources, the optimal method to improve the permeability of r-NF membranes was identified.