Article
Chemistry, Analytical
Andrew P. Burns, Ya-Qin Zhang, Tuan Xu, Zhengxi Wei, Qin Yao, Yuhong Fang, Valeriu Cebotaru, Menghang Xia, Matthew D. Hall, Ruili Huang, Anton Simeonov, Christopher A. LeClair, Dingyin Tao
Summary: The development of a highly automated universal sample preparation platform has significantly improved the efficiency of proteomics sample preparation, enabling high-throughput extraction and analysis of proteins from various human cell types. This platform demonstrates excellent digestion efficiency, reproducibility, and universality in quantifying target proteins, showcasing its potential for clinical research.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Yan Chen, Nurgul Kaplan Lease, Jennifer W. Gin, Tadeusz L. Ogorzalek, Paul D. Adams, Nathan J. Hillson, Christopher J. Petzold
Summary: The article introduces a sample preparation protocol for bottom-up proteomic analysis of Gram-negative bacterial and fungal cells, using automated liquid handler systems to rapidly and with low variance prepare a large number of samples for protein trypsin digestion in a short time, providing reliable and reproducible proteomic samples.
Article
Multidisciplinary Sciences
Jongmin Woo, Sarah M. Williams, Lye Meng Markillie, Song Feng, Chai-Feng Tsai, Victor Aguilera-Vazquez, Ryan L. Sontag, Ronald J. Moore, Dehong Hu, Hardeep S. Mehta, Joshua Cantlon-Bruce, Tao Liu, Joshua N. Adkins, Richard D. Smith, Geremy C. Clair, Ljiljana Pasa-Tolic, Ying Zhu
Summary: This study introduces a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based single-cell proteomics workflow. The N2 chip enables robust quantification of approximately 1500 proteins and reveals membrane protein markers, demonstrating high stability of single-cell proteome profiles for cells cultured under identical conditions.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Cristian Azorin, Juan L. Benede, Alberto Chisvert
Summary: This study introduces a miniaturized stir bar sorptive dispersive microextraction (mSBSDME) method for analyzing low-availability samples. The method significantly reduces the amount of sorbent and sample, allowing for fast, affordable, portable, and high-throughput analysis of low-volume samples.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Xiaoyue Tang, Xiaoping Xiao, Haidan Sun, Shuxin Zheng, Xiaolian Xiao, Zhengguang Guo, Xiaoyan Liu, Wei Sun
Summary: In this study, a urinary sample preparation method, DRA-Urine, was developed for direct reduction/alkylation of proteins in urine, and showed better results compared to other methods. Adapting this method to a 96-well format, 96DRA-Urine, improved sample preparation throughput while maintaining similar proteomic performance. This method was then used for biomarker discovery in bladder cancer urine, showing promising results.
JOURNAL OF PROTEOMICS
(2022)
Article
Computer Science, Information Systems
Zach E. Nichols, Lahari Saha, Rachael Knoblauch, Tonya M. Santaus, Chris D. Geddes
Summary: This paper investigates the design of a microplate for rapid and high-throughput sample preparation to assist diagnostic assays using FDTD simulations and thermographic imaging experiments. The results show that by adhering passive scattering elements (PSEs) to the bottom of polystyrene microplates and irradiating them in a microwave cavity, similar electromagnetic and thermal enhancements to microwave lysing triangles (MLTs) can be achieved.
Article
Biochemistry & Molecular Biology
Julia M. Malinowska, Taina Palosaari, Jukka Sund, Donatella Carpi, Gavin R. Lloyd, Ralf J. M. Weber, Maurice Whelan, Mark R. Viant
Summary: This study presents an automated sample preparation and analysis workflow for in vitro metabolomics of HepaRG cells using high-resolution mass spectrometry. The workflow demonstrates good repeatability and high sample throughput, which can advance the application of metabolomics in chemical safety.
Article
Medicine, Research & Experimental
Pongkwan Sitasuwan, Thomas W. Powers, Tiffany Medwid, Yuting Huang, Bradley Bare, L. Andrew Lee
Summary: The multi-attribute method (MAM) is a recent advancement in liquid chromatography-mass spectrometry for simultaneous monitoring of multiple product quality attributes in the pharmaceutical industry. While MAM offers automated data processing and reporting, its sample preparation remains cumbersome and low throughput.
Article
Biochemical Research Methods
Yuko Ogata, Pamela M. Quizon, Nancy S. Nightlinger, Pongkwan Sitasuwan, Casey Snodgrass, L. Andrew Lee, Jeffrey D. Meyer, Richard S. Rogers
Summary: The study presented a fully automated MAM sample preparation protocol, achieving rapid desalting using miniaturized size-exclusion chromatography columns on an automated liquid handler. Compared to manual preparation, this automated method showed no significant change in product attributes and their quantities, while enhancing sample recovery and reproducibility.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2022)
Article
Chemistry, Multidisciplinary
Jiayi Lu, Hao Jiang, Yuyi Yan, Zhiwen Zhu, Fengru Zheng, Qiang Sun
Summary: One of the contemporary challenges in materials science is the rapid screening and discovery of materials. High-throughput parallel synthesis can generate experimental sample libraries to facilitate quick material discoveries. Molecular self-assembly on surfaces has proved to be a useful method for constructing nanostructures with interesting properties or topologies. However, high-throughput preparations of supramolecular surface nanostructures have been less explored.
Review
Spectroscopy
Qin Fu, Christopher I. Murray, Oleg A. Karpov, Jennifer E. Van Eyk
Summary: Sample preparation for mass spectrometry-based proteomics is time-consuming and prone to analytical errors, especially the proteolytic digestion step. Automated liquid handling workstations offer a reliable solution for sample processing, with diligent assessment of sample type, protocol design, reagents, and incubation conditions improving speed and consistency. Automated sample preparation facilitates increased throughput and reproducible quantitation of biomarker candidates, which is essential for processing large patient cohorts to validate potential clinical applications.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Microbiology
Todd M. Pryce, Erin J. Haygarth, Jessica Bordessa, Courtney T. Jeffery, Ian D. Kay, James P. Flexman, Peter A. Boan
Summary: High-throughput extraction-free sample preparation method (Direct) using the PlexPCR SARS-CoV-2 assay is proposed as an alternative approach for large-scale population testing for SARS-CoV-2. Compared to the gold standard technique (nucleic acid extraction), Direct method shows high overall agreement and sensitivity. By combining cobas, Plex, and Direct, a high throughput of 19,364 results can be achieved in a 24-h period.
MICROBIOLOGY SPECTRUM
(2022)
Review
Biochemical Research Methods
Zhenbin Zhang, Minyang Zheng, Yufen Zhao, Perry G. Wang
Summary: The sensitivity and accuracy of proteomics analysis are determined by sample preparation and separation methods. This article comprehensively reviews recent advancements in high-throughput and high-sensitivity techniques for sample preparation and separation in proteomics research.
Article
Chemistry, Multidisciplinary
Jiaxi Peng, Calvin Chan, Shuailong Zhang, Alexandros A. Sklavounos, Maxwell E. Olson, Erica Y. Scott, Yechen Hu, Vigneshwar Rajesh, Bingyu B. Li, M. Dean Chamberlain, Shen Zhang, Hui Peng, Aaron R. Wheeler
Summary: This study reports the development of an All-in-One digital microfluidic (DMF) pipeline for proteomic sample analysis. The pipeline allows for automated sample reduction, alkylation, digestion, isotopic labeling, and analysis. The integration of dimethyl labeling enables relative quantification of trace samples at the nanogram level. The All-in-One pipeline shows potential for evaluating mass-limited samples and could be useful for proteomic cancer sub-typing.
Article
Biotechnology & Applied Microbiology
Weitao Shen, Yue Yu, Rong Zhou, Ninghui Song, Ping Wan, Zhenyan Peng, Ran Liu, Yuanqing Bu
Summary: This study analyzed the bacterial and pathogen composition and diversity in fecal samples and digestates using three mesophilic anaerobic fermentation methods. The results showed that different fermentation methods had different effects on the composition and diversity, with the traditional fermentation method having the least impact.
ENVIRONMENTAL TECHNOLOGY & INNOVATION
(2022)
Article
Biochemical Research Methods
Saadia Ouzia, Anne-Lise Royer, Marzia Pezzolato, Alessandro Benedetto, Elena Biasibetti, Yann Guitton, Bruno Le Bizec, Elena Bozetta, Gaud Dervilly
Summary: Through a study using reversed phase liquid chromatography-electrospray ionization-high-resolution mass spectrometry, specific patterns and candidate biomarkers associated with three steroid treatments in bovine urine profiles were identified. Level-1 identification of two biomarkers related to energy pathways and skeletal muscle functioning was achieved through MS-2 structural elucidation.
DRUG TESTING AND ANALYSIS
(2022)
Article
Biochemical Research Methods
Chloe Cloteau, Gaud Dervilly, Zied Kaabia, Florian Bagilet, Vivian Delcourt, Benoit Loup, Yann Guitton, Anne-Lise Royer, Fabrice Monteau, Patrice Garcia, Marie-Agnes Popot, Bruno Le Bizec, Ludovic Bailly-Chouriberry
Summary: A non-targeted metabolomics approach was used to identify potential biomarkers associated with the abuse of Anabolic-Androgenic Steroids in animal competitions using equine urine samples. The model's performances and robustness were successfully preserved in a high-throughput liquid chromatography-selected reaction monitoring method. The transferability of the method to a second laboratory demonstrated its applicability in developing biomarker-based strategies for doping control.
DRUG TESTING AND ANALYSIS
(2022)
Article
Environmental Sciences
Komodo Matta, Tiphaine Lefebvre, Evelyne Vigneau, Veronique Cariou, Philippe Marchand, Yann Guitton, Anne-Lise Royer, Stephane Ploteau, Bruno Le Bizec, Jean-Philippe Antignac, German Cano-Sancho
Summary: The study confirmed positive associations between certain persistent organic pollutants and the risk of endometriosis, utilizing various analytical methods to identify the effects of POPs on the disease.
ENVIRONMENT INTERNATIONAL
(2022)
Article
Food Science & Technology
Axel Raux, Emmanuelle Bichon, Alessandro Benedetto, Marzia Pezzolato, Elena Bozzetta, Bruno Le Bizec, Gaud Dervilly
Summary: Recombinant bovine growth hormone (rbGH) is widely used to stimulate milk production in dairy animals, and detecting its presence in milk poses several challenges that require sensitive analytical strategies.
Article
Environmental Sciences
Maykel Hernandez-Mesa, Luca Narduzzi, Sadia Ouzia, Nicolas Soetart, Laetitia Jaillardon, Yann Guitton, Bruno Le Bizec, Gaud Dervilly
Summary: Recent epidemiological studies have shown that current levels of exposure to polychlorinated biphenyls (PCBs) remain a significant health concern, especially for non-dioxin-like PCB exposure. This study used pigs as an animal model to investigate the effects of Aroclor 1260 exposure, resulting in the bioaccumulation of NDL-PCBs in pig fat and the identification of biomarkers related to PCB exposure through metabolomics and lipidomics.
Article
Environmental Sciences
C. Simonnet-Laprade, S. Bayen, D. McGoldrick, T. McDaniel, S. Hutinet, P. Marchand, A. Venisseau, R. Cariou, B. Le Bizec, G. Dervilly
Summary: This study explored the complementarity between targeted and non-targeted screening based on liquid and gas-phase chromatography coupled to mass spectrometry for the comprehensive characterization of organohalogen fingerprints in Lake Ontario lake trout samples. The results showed that targeted screening highlighted more halogenated compounds, while non-targeted screening extended the screening to unknown halogenated compounds.
Article
Chemistry, Applied
Christelle Planche, Jeremy Ratel, Frederic Mercier, Cheng Zhang, Magaly Angenieux, Patrick Blinet, Philippe Marchand, Gaud Dervilly, Isabelle Albert, Jessica Tressou, Laurent Debrauwer, Erwan Engel
Summary: This study assessed the bioaccessibility of PCBs in meat using in vitro digestion and multianalyte methods, revealing that fat content, cooking conditions, and consumer age all influence the bioaccessibility of PCBs. Bayesian analysis showed that higher fat content, well-done cooking, and older age result in lower bioaccessibility of PCBs.
Article
Medicine, General & Internal
Luc Colas, Anne-Lise Royer, Justine Massias, Axel Raux, Melanie Chesneau, Clarisse Kerleau, Pierrick Guerif, Magali Giral, Yann Guitton, Sophie Brouard
Summary: This is an open access article published by Elsevier B.V., under the copyright of the authors and licensed under CC BY-NC-ND.
Article
Environmental Sciences
Charlotte Corporeau, Sebastien Petton, Romain Vilaca, Lizenn Delisle, Claudie Quere, Valerian Le Roy, Christine Dubreuil, Sandra Lacas-Gervais, Yann Guitton, Sebastien Artigaud, Benoit Bernay, Vianney Pichereau, Arnaud Huvet, Bruno Petton, Fabrice Pernet, Elodie Fleury, Stephanie Madec, Christophe Brigaudeau, Catherine Brenner, Nathalie M. Mazure
Summary: This study compared intertidal oysters with subtidal oysters and found that intertidal oysters at different depths delayed the onset of mortality associated with POMS. Despite slower growth, intertidal oysters showed increased resistance through metabolic, inflammatory, and immune responses, improving their overall health.
MARINE ENVIRONMENTAL RESEARCH
(2022)
Article
Biochemical Research Methods
Max L. Feuerstein, Maykel Hernandez-Mesa, Andrea Kiehne, Bruno Le Bizec, Stephan Hann, Gaud Dervilly, Tim Causon
Summary: This study compared the collision cross section (CCS) derived from three different IM-MS technologies for the analysis of steroids and small molecules. The interlaboratory performance was found to be excellent, but differences in ion conformation sampled on different instrument types need further investigation.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Environmental Sciences
Beate Escher, Marja Lamoree, Jean-Philippe Antignac, Martin Scholze, Matthias Herzler, Timo Hamers, Tina Kold Jensen, Marc Audebert, Francois Busquet, Dieter Maier, Michael Oelgeschlaeger, Maria Joao Valente, Henriette Boye, Sebastian Schmeisser, Gaud Dervilly, Matteo Piumatti, Solene Motteau, Maria Koenig, Kostja Renko, Maria Margalef, Ronan Cariou, Yanying Ma, Andreas Frederik Treschow, Andreas Kortenkamp, Anne Marie Vinggaard
Summary: The European Union's Green Deal aims to address the risk of chemical mixtures to human health by filling the existing gaps in risk assessment and implementing regulatory measures. To tackle this challenge, the PANORAMIX project suggests characterizing real-life mixtures, developing a high-throughput screening strategy, evaluating concern levels for children's development, and creating a web-based interface for risk estimation.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Environmental Sciences
Mathilde Godere, Philippe Marchand, Anais Venisseau, Ingrid Guiffard, Jean-Charles Leblanc, Bruno Le Bizec, Gaud Dervilly
Summary: There has been a recent revival of interest in historical contaminants such as PCNs. This study assessed the presence of PCNs in fish and seafood products in France and found that they were present in all samples, with levels similar to those in other European regions. Compared to other pollutants, PCNs were observed to contribute less to total concentrations.
Article
Medicine, Research & Experimental
Thibault Leger, Aurelien Brun, Kassandra Lanchais, Jean-Paul Rigaudiere, Arnaud Briat, Yann Guitton, Fabien Marchand, Anne Tournadre, Frederic Capel
Summary: This study found that nutritional supplementation with omega 3 fatty acids can alleviate symptoms of rheumatoid arthritis and be an effective preventive treatment for patients who do not need pharmacological therapy.
