Article
Chemistry, Analytical
Tanja Bien, Sebastian Bessler, Klaus Dreisewerd, Jens Soltwisch
Summary: Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has the potential to visualize the spatial distribution of biomolecules in cell cultures and tissue sections with high resolution, but sample preparation is crucial. A study found that a robust sample preparation protocol can preserve cell morphology and molecular integrity, contributing to the study of cell-to-cell heterogeneities at a molecular level. Advancements in single-cell MALDI imaging could benefit from these protocols.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Lianlian Ma, Qingrong Xie, Mingyi Du, Yudi Huang, Yingying Chen, Dong Chen, Yizhu Xu, Hanhong Xu, Xinzhou Wu, Zhibin Yin
Summary: This study systematically investigated the optimized sample preparation conditions for insects and model organisms in mass spectrometry imaging (MSI), providing guidelines for MSI analysis and expanding its potential in life sciences and environmental sciences.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Chenyu Yang, Ran Wu, Haiqiang Liu, Liang Qin, Lulu Chen, Hualei Xu, Hao Hu, Jinrong Li, Hua Guo, Yiyang Shi, Dongxu Jiang, Qichen Hao, Jinchao Feng, Yijun Zhou, Xiangyi Liu, Gaopeng Li, Xiaodong Wang
Summary: In this study, polyacrylamide gel (PAAG) was successfully used as a new embedding medium for enhancing tissue imaging of metabolites via matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). The results showed that PAAG embedding has advantages over commonly-used embedding media, including better morphology maintenance, absence of interference below m/z 2000, and more efficient ionization of metabolites. PAAG embedding has the potential to become a standard practice for metabolite MALDI tissue imaging, expanding the application scope of MALDI-MSI.
CHEMICAL COMMUNICATIONS
(2023)
Article
Environmental Sciences
Parvaneh Hajeb, Linyan Zhu, Rossana Bossi, Katrin Vorkamp
Summary: Recent advances in mass spectrometers have enabled the detection of a wide range of organic compounds in a single procedure, leading to increased attention on suspect and non-target screening techniques. Sample preparation is crucial, but there is a lack of generic protocols in this rapidly growing analytical field.
Article
Biochemical Research Methods
Rafael Oliveira Martins, Giovanna Lopes de Araujo, Carla Santos de Freitas, Allyster Rodrigues Silva, Rosineide Costa Simas, Boniek Gontijo Vaz, Andrea Rodrigues Chaves
Summary: Analytical methods like liquid chromatography and mass spectrometry are commonly used for compound analyses, but facing challenges in complex matrices. Miniaturized sample preparation methods offer simplicity and effectiveness in addressing difficult sample preparation steps.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Chemistry, Analytical
Harvey E. Johnston, Kranthikumar Yadav, Joanna M. Kirkpatrick, George S. Biggs, David Oxley, Holger B. Kramer, Rahul S. Samant
Summary: Complete and reproducible extraction of protein is crucial for proteome analysis. Solvent precipitation SP3 (SP4) is proposed as an alternative method, which captures protein aggregates by centrifugation instead of magnetism. SP4 provides equivalent or higher protein yields and improved reproducibility. It also recovers more low-solubility and transmembrane proteins, offering higher recovery rates.
ANALYTICAL CHEMISTRY
(2022)
Review
Chemistry, Analytical
Yuan Zhao, Di Chen, Hongyu Duan, Peiwu Li, Wenqin Wu, Xiuping Wang, Amnart Poapolathep, Saranya Poapolathep, Antonio F. Logrieco, Michelangelo Pascale, Cheng Wang, Zhaowei Zhang
Summary: This study focuses on the determination of mycotoxins, hazardous fungi, and their metabolites using mass spectrometry (MS) techniques. Sample preparation techniques for mycotoxins and fungi were evaluated, and the identification of mycotoxins and the hazardous metabolism of fungi in humans, plants, and animals were discussed. The merits of diversified MS techniques and their sensitivity and feasibility were also discussed, and challenges and opportunities are suggested.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Analytical
Joao Raul Belinato, Vinicius Ricardo Acquaro, Luciana Teresa Dias Cappelini, Fabio Augusto
Summary: The interest in bioactive compounds from microorganisms has increased since the first discovery, with microorganisms being a key source of biomolecules with diverse applications. While conventional sample preparation techniques are still widely used, microextraction techniques show promise in overcoming limitations and promoting a deeper understanding of complex systems and the discovery of new molecules.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Simon J. S. Cameron, Alvaro Perdones-Montero, Lieven Van Meulebroek, Adam Burke, Kate Alexander-Hardiman, Daniel Simon, Richard Schaffer, Julia Balog, Tamas Karancsi, Tony Rickards, Monica Rebec, Sara Stead, Lynn Vanhaecke, Zoltan Takats
Summary: This study introduces an automated sample-preparation-free mass spectrometry platform utilizing a CO2 laser for sample thermal desorption, achieving high signal-to-noise ratios. The platform is suitable for analyzing three diverse biological materials and has shown promise in clinical microbiology, diabetes research, and food authenticity testing.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Analytical
Fujia Wang, Tim Veth, Marije Kuipers, Maarten Altelaar, Kelly E. Stecker
Summary: A successful mass spectrometry-based phosphoproteomics analysis relies on effective sample preparation strategies. The performance of the S-Trap protocol for phosphoproteomics studies is unclear, and the addition of phosphoric acid (PA) in the existing protocol is detrimental to downstream phosphopeptide enrichment. This study systematically evaluates the performance of the S-Trap digestion for proteomics and phosphoproteomics, and demonstrates that an optimized S-Trap approach, with trifluoroacetic acid substituted for PA, is a simple and effective method for phosphoproteomics sample preparation.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Fenglin Shen, Yueting Xiong, Lei Zhang, Hengchao Li, Huanhuan Zhao, Xiaohui Liu, Pengyuan Yang
Summary: A new rapid and simple sample preparation method was developed for serum proteomic studies, allowing for efficient identification of multiple proteins in under 2 hours. This method has the potential to accelerate biomarker discovery and clinical application in serum protein research.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
John B. Coulton, James L. Edwards
Summary: The sample preparation technique described in the study involves online filter-assisted electroporation-based cell lysis and chilled organic solvent extraction for rapid preparation of metabolomic samples from suspended cells. By using isotopically labeled internal standards and C-13-glucose labeling experiments, the method ensures enzymatic quenching and successful incorporation of C-13 into organic acid metabolites. Analysis by nano-reverse-phase liquid chromatography-mass spectrometry (nano-RP-LC-MS) demonstrates the effectiveness of the technique in studying metabolites such as itaconate.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Food Science & Technology
Chuanqin Hu, Xinyu Song, Zhenzhen Shao, Yingli Liu, Jing Wang, Baoguo Sun
Summary: Untargeted metabolomics was used in this study to investigate the effects of Mep on the metabolic profile of adipose tissue in Sprague-Dawley rats. Twenty-six differential metabolites and eight major perturbed metabolic pathways were identified, including linoleic acid metabolism, Phenylalanine, tyrosine, and tryptophan biosynthesis, phenylalanine metabolism, arachidonic acid metabolism, Glycine, serine, and threonine metabolism, glycerolipid metabolism, Alanine, aspartate, and glutamate metabolism, and glyoxylate and dicarboxylic acid metabolism. This study provides a solid foundation for understanding the toxic mechanism of Mep.
Article
Biochemical Research Methods
Li Chen, Wenyun Lu, Lin Wang, Xi Xing, Ziyang Chen, Xin Teng, Xianfeng Zeng, Antonio D. Muscarella, Yihui Shen, Alexis Cowan, Melanie R. McReynolds, Brandon J. Kennedy, Ashley M. Lato, Shawn R. Campagna, Mona Singh, Joshua D. Rabinowitz
Summary: NetID is a novel global network optimization approach for annotating untargeted LC-MS metabolomics data. By combining known biochemical and metabolomic principles, it significantly enhances annotation coverage and accuracy, facilitating the discovery of metabolites.
Article
Biochemical Research Methods
Stephanie Biedka, Brigitte F. Schmidt, Nolan M. Frey, Sarah M. Boothman, Jonathan S. Minden, Amber Lucas
Summary: This study presents a new protein sample preparation method, ProMTag, which enables whole proteome capture, cleanup, and release of intact proteins, as well as generation of peptides for downstream analysis. The ProMTag workflow yields high percentages for both intact proteins and proteome digests, making it a versatile and high-quality approach for proteome sample preparation.
JOURNAL OF PROTEOME RESEARCH
(2021)
Editorial Material
Chemistry, Analytical
Jonathan Sweedler
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Yuxuan Richard Xie, Varsha K. Chari, Daniel C. Castro, Romans Grant, Stanislav S. Rubakhin, Jonathan V. Sweedler
Summary: Improved throughput and lower detection limits have enabled single-cell chemical analysis to characterize different functional states of individual cells. Image-guided single-cell mass spectrometry leverages microscopy for high-throughput analysis of cellular targets. This study proposes DATSIGMA, a data-driven and machine learning workflow for enhanced interpretation of complex single-cell mass spectrometry data, which has been successfully tested on various biological applications, including brain cell classification. Due to its open-source nature, DATSIGMA allows for customization and adaptation to other types of single-cell mass spectrometry data.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Medicinal
Jin Jia, Dharmeshkumar Parmar, Joanna F. Ellis, Tianyuan Cao, Allison R. Cutri, Joshua D. Shrout, Jonathan V. V. Sweedler, Paul W. Bohn
Summary: This study investigates the effect of surface properties on quorum sensing and virulence factors in Pseudomonas aeruginosa, especially the differences between mucoid and non-mucoid strains. The results show that mucoid strains have a higher sensitivity to quinolone signals induced by surface mucin patterning. Additionally, phenazine virulence factors are observed in pellicle biofilms of both mucoid and non-mucoid strains but not in static biofilms.
ACS INFECTIOUS DISEASES
(2023)
Article
Chemistry, Analytical
Shipeng Sun, Weiwei Tang, Bin Li
Summary: In this study, a label-free and automatic approach for the characterization and identification of herbal powders and their adulterants was developed. The method combined microscopy-guided auto-sampling and matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) to provide both morphological identification and chemical profiles. A gelatin coating on the glass slide immobilized the dried herbal powders, allowing for in situ extraction and preventing diffusion. Optical microscopy was used to acquire microstructure information, and software was employed to select candidate powders for MALDI-MS identification. The combination of microstructure features and chemical profiles greatly enhanced the authentication capability of microscopy.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Shuaizhen Zhou, Zia Fatma, Pu Xue, Shekhar Mishra, Mingfeng Cao, Huimin Zhao, Jonathan Sweedler
Summary: To meet the increasing need for high-throughput screening in metabolic engineering, a fast and information-rich screening method is required. Liquid extraction surface analysis coupled with mass spectrometry (LESA-MS) is an efficient approach that directly samples and introduces metabolites from a surface to MS. In this study, LESA-MS combined with an acoustic liquid handler and stable isotope-labeled internal standards, enabling absolute quantitation of target chemicals and high-throughput screening for microbial metabolites.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Jonathan V. Sweedler, Dong-Kyu Lee, Stanislav S. Rubakhin
Summary: Approaches for protein/peptide characterization in single cells of formaldehyde-fixed tissues via mass spectrometry are still being developed. The lack of a general method to eliminate formaldehyde-induced crosslinking is a major challenge. A workflow was established for high-throughput peptide profiling of single cells from formaldehyde-fixed pancreatic tissues, enabling the analysis of 2594 single islet cells and detection of 28 peptides, including insulin C-peptides and glucagon. This workflow expands the sample availability for single-cell MS characterization to a wide range of formaldehyde-fixed tissues stored in biobanks.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Weiwei Tang, Jun-Jie Shi, Wei Liu, Xu Lu, Bin Li
Summary: A matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) assisted genome mining strategy was applied to discover a glycosyltransferase (GT) named PgGT1 from the root of Platycodon grandiflorum. PgGT1 was found to catalyze the synthesis of platycoside E (PE) by sequentially attaching two beta-1,6-linked glucosyl residues to the glucosyl residue at the C3 position of platycodin D (PD). The study also revealed the crucial roles of residues S273, E274, and H350 in stabilizing the sugar donor and positioning the glucose for optimal glycosylation. These findings provide insights into the biosynthetic pathway of PE and have potential implications in industrial biotransformation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Kisurb Choe, Michael A. Jindra, Susan C. Hubbard, Brian F. Pfleger, Jonathan Sweedler
Summary: By screening ozonolysis products of membrane lipids from Escherichia coli colonies using a rapid MS assay, we identified two variants with altered regiospecificity of the desaturase gene, which were able to influence the membrane composition and fatty acid distribution of E. coli strains. Additionally, we demonstrated the production of only saturated free fatty acids using a deficient chassis expressing a non-native acyl-ACP desaturase and a medium-chain thioesterase.
ANALYTICAL BIOCHEMISTRY
(2023)
Article
Chemistry, Analytical
Ruiyang Sun, Weiwei Tang, Ping Li, Bin Li
Summary: In this study, an efficient and fast on-tissue chemical derivatization (OTCD) approach was developed to pinpoint the locations of C=C bonds in complex lipids in situ. The OTCD method provided rich structural information on lipid C=C location isomers, and their accurate spatial distribution patterns were resolved in biological tissues.
ANALYTICAL CHEMISTRY
(2023)
Article
Biophysics
Xian-Na Wang, Yahui Song, Weiwei Tang, Ping Li, Bin Li
Summary: Microfluidic technology provides an ideal platform for in situ screening of enzyme inhibitors and activators from natural products. This study developed a surface-modified ITO glass-PDMS hybrid microfluidic chip, which integrated fluorescence imaging and MALDI MSI for evaluating thrombin interaction with potential inhibitors. The results showed that luteolin, cynaroside, and baicalin have good thrombin inhibitory activity, making them promising candidates for further research in developing inhibitors for thrombin-related diseases.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Biology
Tian (Autumn) Qiu, Cindy J. Lee, Chen Huang, Dong-Kyu Lee, Stanislav S. Rubakhin, Elena V. Romanova, Jonathan V. Sweedler
Summary: The microbial metabolite d-alanine, derived from food and gut microbiota, accumulates in the pancreas, brain, and pituitary of mice. The sources of d-alanine in mice are shown to be microbiota and diet, rather than endogenous racemization. This research highlights the importance of investigating the biological functions of gut-microbiome derived d-alanine, especially its role in NMDAR-related activities in the microbiome-gut-brain axis.
COMMUNICATIONS BIOLOGY
(2023)
Article
Nanoscience & Nanotechnology
Abigail A. Weaver, Dharmeshkumar Parmar, Ella A. Junker, Jonathan V. Sweedler, Joshua D. Shrout
Summary: Investigated the distribution patterns of rhamnolipid congeners and their differences in cell-free environments and colony biofilms. Found that congeners exhibit distinct distribution patterns on surfaces, with shorter fatty acid chains being more centrally located and longer chains exhibiting more heterogeneity and distal distribution. Congeners with similar structures can distribute differently. The distribution patterns of individual congeners within colony biofilms are diverse, with multiple local microenvironments of varied congener composition.
ACS APPLIED BIO MATERIALS
(2023)
Review
Multidisciplinary Sciences
Roland Hellinger, Arnar Sigurdsson, Wenxin Wu, Elena V. Romanova, Lingjun Li, Jonathan V. Sweedler, Roderich D. Suessmuth, Christian W. Gruber
Summary: Peptidomics combines genomics, modern proteomics, analytical chemistry, and computational biology techniques for peptide discovery and characterization. Peptides are biopolymers composed of 2-50 amino acids, often produced by cellular machinery or enzymes. They play important physiological roles as signaling molecules and toxins, and have emerging applications in biomarker discovery and therapeutics. Peptidomics involves qualitative and quantitative analysis of peptides in biological samples using a specialized set of tools and workflows.
NATURE REVIEWS METHODS PRIMERS
(2023)
Article
Chemistry, Analytical
Weiwei Tang, Yuejie Zhang, Ping Li, Bin Li
Summary: In this study, an integrated strategy combining quadruple single-pass intestinal perfusion (Q-SPIP) technique and matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) was developed for in situ visualization and assessment of drug absorption and interaction in rat intestines. The Q-SPIP model enabled simultaneous perfusion of four individual segments of each rat intestine, providing rich data for analysis. The optimized MALDI MSI approach accurately visualized the drug distribution and absorption in rat intestinal tissue. The findings demonstrate the utility and versatility of Q-SPIP coupled with MALDI MSI in studying transporter-mediated intestinal drug absorption and interaction.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Yuxuan Richard Xie, Varsha K. Chari, Daniel C. Castro, Romans Grant, Stanislav S. Rubakhin, Jonathan V. Sweedler
Summary: Improved throughput and enhanced detection limits enable researchers to characterize the functional states of individual cells using single-cell chemical analysis. Image-guided single-cell mass spectrometry combines optical microscopy and fluorescence microscopy to analyze cellular and subcellular targets. In this study, a data-driven and machine learning workflow called DATSIGMA was proposed for feature extraction and interpretability of complex single-cell mass spectrometry data. The toolset was successfully implemented and tested on various experimental data sets, showing its potential for diverse biological applications.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Food Science & Technology
Peiling Yan, Weiqing Lan, Jing Xie
Summary: Sodium alginate (SA) is an important marine polysaccharide that has extensive applications in food preservation and quality maintenance. Modification methods can be used to improve the properties of SA and make it compatible with other materials. Solvent-casting films and gels are common methods for using modified SA in food preservation.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2024)
Article
Food Science & Technology
Zhihui Yu, Yating Gao, Xinyi Jia, Shuai Cui, Li Ma, Dan Zheng, Xin Li, Long Li, Lixin Zhang, Yisheng Chen
Summary: This review provides a new perspective on the state-of-the-art research and application of high-intensity ultrasound (HIU) for modifying blue food proteins (BFPs). The effects of HIU treatment on the functional properties and structural composition of BFPs are comprehensively evaluated.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2024)
Review
Food Science & Technology
Honghong Zhang, Haoran Fan, Xueming Xu, Dan Xu
Summary: This review provides a comprehensive summary of changes in different components in frozen dough, including starch, gluten protein, lipid, and yeast, from a multiscale perspective. The methods of improving the production process of frozen dough, from main materials to end products, have been discussed. Key findings include the use of high gluten strength wheat flour and composite flour with high dietary fiber to improve the freezing resistance of gluten-starch matrix, as well as various methods to improve yeast freeze tolerance and the effects of different freezing rates.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2024)
Article
Food Science & Technology
Junhua Xie, Qiqiong Li, Shaoping Nie
Summary: This review provides an overview of bEVs' biology, evidence for their health benefits, and possible molecular pathways involved in their health-promoting effects, as well as perspectives for applications in foods and pharmaceuticals.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2024)
Article
Food Science & Technology
Jose Bueno-Mancebo, Adriana Artola, Raquel Barrena, Fernando Rivero-Pino
Summary: This review provides an overview of the characterization, production, and applications of sophorolipids (SLs) in the food industry. SLs exhibit bioactivity and environmental friendliness, making them suitable for various applications in food packaging, agriculture, and other areas. The importance of SLs in the context of the One Health approach is emphasized.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2024)
Letter
Food Science & Technology
Saurabh Singh
Summary: This paper is interesting and relevant to determining the moisture content of food products. However, it lacks the classification of oven drying methods, which are cost-effective and important for drying solids and semisolids.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2024)
Article
Food Science & Technology
Yong Cheng, Beijun Ang, Chaoyi Xue, Zhenyu Wang, Liduan Yin, Tong Wang, Qiuming Chen, Zhaojun Wang, Maomao Zeng, Wei Zhang, Jie Chen, Zhiyong He
Summary: Pollen fermentation can improve its nutrient profile, degrade allergenic compounds, enhance bioavailability, and promote gut health. Pollen can serve key roles in fermented food production and create opportunities for innovative product development. However, quality and safety considerations are important in pollen fermentation.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2024)
Review
Food Science & Technology
Fanghua Guo, Fereidoon Shahidi
Summary: This contribution summarizes the potential of anthocyanins as alternatives to antibiotics, focusing on their anti-oxidation, anti-inflammation, absorption, metabolism, antibacterial effects, and the possible mechanisms behind these effects. The use of encapsulation to improve stability and bioavailability of anthocyanins, as well as targeted delivery to the lower digestive tract, shows promise in replacing antibiotics. However, more in vivo studies are needed to further support these findings.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2024)
Article
Food Science & Technology
Muhammad Rehan Khan, Elena Torrieri, Florent Allais, Sami Fadlallah
Summary: This opinion paper explores the potential of integrating synthetic biology into microbial polymers to produce tailored biopolymers for food packaging applications. By leveraging synthetic biology tools and adopting safety assessment protocols established within the regulatory framework, this innovative approach has the potential to not only replace conventional methods but also address environmental concerns associated with traditional food packaging.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2024)