Article
Chemistry, Analytical
Ahmed Ben Faleh, Stephan Warnke, Teun Van Wieringen, Ali H. Abikhodr, Thomas R. Rizzo
Summary: The combination of high-resolution ion mobility spectrometry and cryogenic vibrational spectroscopy offers a rapid and efficient method for separating and identifying isomeric and isobaric metabolites. Ion mobility enables the separation of isomers in milliseconds, while cryogenic IR spectroscopy provides clear IR fingerprints for molecular identification. Additionally, our approach allows for automatic identification of metabolite isomers by comparing their IR fingerprints with those in a database, eliminating the need for analytical standards. We demonstrate the principle of this approach by constructing a database of IR fingerprints for eight isomeric/isobaric metabolites and using it for identification in mixtures. Furthermore, our fast IR fingerprinting technology allows for rapid probing of IR fingerprints as molecules elute from an LC column. This approach has great potential to enhance metabolomics workflows in terms of accuracy, speed, and cost.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Andras Guttman, Csenge Filep, Barry L. Karger
Summary: Recent advancements in protein therapeutics necessitate high-resolution bioseparation techniques, such as SDS-CGE using a borate cross-linked dextran matrix. By adjusting the dextran and borate concentration ratios, optimal separation for specific biopharmaceutical modalities can be achieved with excellent reproducibilities.
ANALYTICAL CHEMISTRY
(2021)
Article
Materials Science, Multidisciplinary
Kimberly Miller McLoughlin, Amin Jamei Oskouei, Michelle K. Sing, Alireza Bandegi, Sarah Mitchell, Jayme Kennedy, Thomas G. Gray, Ica Manas-Zloczower
Summary: Cross-linked EVA is widely used in demanding applications and its thermomechanical properties are influenced by various factors. The content of vinyl acetate, molecular weight, and chain topology affect the crystallinity and crystallite size of the material. Cross-linking reduces the crystallinity compared to un-cross-linked EVA. By controlling the properties and degree of cross-linking, the performance properties of cross-linked EVA can be adjusted. Understanding these effects enables material selection and property adjustment to meet the demands of different applications.
ACS APPLIED POLYMER MATERIALS
(2023)
Article
Chemistry, Physical
Simon Lemcke, Joern H. Appeldorn, Michael Wand, Thomas Speck
Summary: In this paper, the authors demonstrate the identification of metastable states in a small peptide through a neural network that utilizes structural information. They show that an autoencoder architecture, EncoderMap, can effectively find a low-dimensional representation solely based on structural information to identify long-lived molecular conformations. The results contribute to computational strategies for exploring the configuration space of peptides and proteins.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Basab Kanti Das, Raju Samanta, Sahnawaz Ahmed, Bapan Pramanik
Summary: A peptide hydrogelator containing a C-terminal cysteine can form insoluble hydrogel through non-covalent and covalent interactions, exhibiting thixotropic and injectable properties. It has been utilized for the removal of organic dyes from wastewater, offering a reliable, straightforward, nontoxic, cheap, and environmentally friendly adsorbent.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Polymer Science
Sarah Hettal, Sebastien Roland, Konsta Sipila, Harri Joki, Xavier Colin
Summary: This study investigates the degradation of silane cross-linked polyethylene filled with varying amounts of aluminum tri-hydrate. The results show that the degradation is more pronounced in the vicinity of the fillers, leading to an increase in chain scissions. The addition of fillers and interfacial degradation also significantly affect the fracture properties of the materials.
Article
Nanoscience & Nanotechnology
Yan Li, Siqi Li, Yujie Shen, Xue Han, Yao Li, Yingchun Yu, Meilan Huang, Xia Tao
Summary: The study utilized a multifunctional agent histidine (His) to modify the SnO2/perovskite interface, reducing interfacial trap state density and nonradiative recombination loss, improving electron extraction/transfer efficiency, and enhancing device performance, leading to superior power conversion efficiency and open-circuit voltage.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Computer Science, Information Systems
Chenhan Zhang, Yuanshao Zhu, Christos Markos, Shui Yu, James J. Q. Yu
Summary: The study proposes a novel semisupervised FL scheme named mean teacher semisupervised FL (MTSSFL) for privacy-protected transportation mode identification. By inserting the global model in the gradient updates of the local models that only have unlabeled data, MTSSFL achieves highly accurate and privacy-protected TMI. Additionally, mean-teacher-averaging is employed as a secure parameter aggregation mechanism to further enhance the global model's performance without extra training.
IEEE INTERNET OF THINGS JOURNAL
(2021)
Article
Chemistry, Medicinal
Baptiste Houyvet, Yolande Bouchon-Navaro, Claude Bouchon, Erwan Corre, Celine Zatylny-Gaudin
Summary: This study identified several AMPs, including new piscidin-like peptides, in lionfish for the first time. These AMPs have potential uses in human health or aquaculture.
Article
Biochemistry & Molecular Biology
I. Schember, M. S. Halfon
Summary: The study successfully predicted enhancers in the A. gambiae genome using a computational method, providing new research tools for tissues affected by malaria transmission and suggesting potential directions for optimizing genetic control methods.
INSECT MOLECULAR BIOLOGY
(2021)
Article
Food Science & Technology
Chiung-Jung Wen, Yen-Chun Koh, Yen-Chen Tung, Pin-Yu Ho, Shu-Chen Hsieh, Yi-Chen Lo, Jaw-Shiun Tsai, Min-Hsiung Pan
Summary: This study aims to explore the relationship between serum metabolites and gut microbiota in non-robust older adults as a potential diagnostic biomarker. The results show significant differences in gut microbial composition between robust and non-robust subjects, particularly with the abundance of Escherichia/Shigella. Moreover, the abundance of Escherichia/Shigella is positively correlated with the levels of discriminant metabolites. These findings indicate the clear interrelation between gut microbiota and serum metabolites in non-robust older adults, suggesting Escherichia/Shigella as a potential biomarker candidate for robustness sub-phenotypic identification.
MOLECULAR NUTRITION & FOOD RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Joel Markgren, Faiza Rasheed, Mikael S. Hedenqvist, Marie Skepo, Eva Johansson
Summary: The aim of this study was to understand the mechanisms behind clustering and cross-linking of gliadins, a type of wheat seed storage protein. The results showed that gliadins exist as monomers and clusters in solution, but form large polymers during drying. Simulation and prediction algorithms revealed different mechanisms for polymer formation and aggregation. These findings have important implications for customized processing using these proteins.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Physical
Zhenchao Li, Qiang Liu, Yirui Deng, Miaomiao Zhou, Wenhao Tang, Huiyou Dong, Wenhui Zhao, Ruiping Liu
Summary: A cross-linked succinonitrile (SN)-based solid-state electrolyte was synthesized to address the low ionic conductivity and unstable electrode interface in solid-state lithium batteries. The quasi-solid gel electrolyte exhibited high electrochemical performance and good interfacial stability. This work opens up new opportunities for designing high-safety electrolytes and enabling the practical application of high-voltage lithium metal batteries. Rating: 9 out of 10.
MATERIALS TODAY ENERGY
(2023)
Article
Biochemistry & Molecular Biology
Kelti A. Smith, Mickael Dang, Alexander E. G. Baker, Tobias Fuehrmann, Ana Fokina, Molly S. Shoichet
Summary: Detachment of fragile cell types cultured on 2D surfaces has been shown to be detrimental to their viability. A reversible cross-linked hydrogel was synthesized for cell culture and differentiation, which is stable and can be cleaved by an external stimulus for injection. The hydrogel demonstrated good stability, enzyme-sensitive degradation, and cytocompatibility with iPSC-derived neural progenitor cells, laying the foundation for broad applicability.
Article
Multidisciplinary Sciences
Lorenzo Pallante, Aigli Korfiati, Lampros Androutsos, Filip Stojceski, Agorakis Bompotas, Ioannis Giannikos, Christos Raftopoulos, Marta Malavolta, Gianvito Grasso, Seferina Mavroudi, Athanasios Kalogeras, Vanessa Martos, Daria Amoroso, Dario Piga, Konstantinos Theofilatos, Marco A. Deriu
Summary: This study developed a novel ML-based algorithm, named VirtuousUmami, that can predict the umami taste of a molecule based on its SMILES representation, providing a more general molecular description. The proposed tool has the potential to rationalize the molecular features underlying umami taste and design peptide-inspired compounds with specific taste properties.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Elke Debrie, Milan Malfait, Ralf Gabriels, Arthur Declerq, Adriaan Sticker, Lennart Martens, Lieven Clement
Summary: Reliable peptide identification is crucial in MS-based proteomics, and the TDA method is widely used for estimating the FDR. However, the assumptions of TDA are often not verified in practice, which can result in poor FDR control and negatively impact downstream data analysis. To address this issue, the TargetDecoy package is introduced, providing necessary functionality to assess the quality and assumptions of TDA for a given set of PSMs.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Ralf Gabriels, Arthur Declercq, Robbin Bouwmeester, Sven Degroeve, Lennart Martens
Summary: There are various output file formats from proteomics search engines, but the lack of standardized formats makes it difficult to process peptide-spectrum matches (PSMs) and PSM files downstream. This article presents psm_utils, a Python package that can handle various PSM file formats and provides a unified and user-friendly interface. It includes a Python API, a command line interface, and a web application for interconverting PSM files and retrieving basic PSM statistics.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Oncology
Ana Teresa Pinto, Ana Beatriz Machado, Hugo Osorio, Marta Laranjeiro Pinto, Rui Vitorino, Goncalo Justino, Catia Santa, Flavia Castro, Tania Cruz, Carla Rodrigues, Jorge Lima, Jose Luis R. Sousa, Ana Patricia Cardoso, Rita Figueira, Armanda Monteiro, Margarida Marques, Bruno Manadas, Jarne Pauwels, Kris Gevaert, Marc Mareel, Sonia Rocha, Tiago Duarte, Maria Jose Oliveira
Summary: Resistance to radiotherapy is a major problem in cancer treatment. Investigating the response of macrophages to ionizing radiation could help overcome tumor radio resistance.
Article
Biochemistry & Molecular Biology
Patrick Willems, Valerie Van Ruyskensvelde, Takanori Maruta, Robin Pottie, Alvaro D. Fernandez-Fernandez, Jarne Pauwels, Matthew A. Hannah, Kris Gevaert, Frank Van Breusegem, Katrien Van der Kelen
Summary: Alternative splicing is an important gene regulatory process in plants, and its inhibition can alleviate cell death and enhance tolerance to oxidative stress.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Chemistry, Analytical
Maxime Gavage, Kaatje Van Vlierberghe, Marc Dieu, Patsy Renard, Thierry Arnould, Kris Gevaert, Marc De Loose, Christof Van Poucke, Anne-Catherine Huet, Nathalie Gillard
Summary: This interlaboratory study evaluated the potential of MS for food allergen detection and quantification using a standard addition quantification strategy and a stable isotope-labeled concatemer as an internal standard. Nine laboratories participated in the study and were able to detect allergens with sufficient sensitivity, although egg detection was more challenging. The encouraging results of this study contribute to harmonization among laboratories testing for allergens.
JOURNAL OF AOAC INTERNATIONAL
(2023)
Article
Biochemical Research Methods
Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwaemmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Tine Claeys, Maxime Menu, Robbin Bouwmeester, Kris Gevaert, Lennart Martens
Summary: Using data from 183 public human data sets, a machine learning model was trained to identify tissue and cell-type specific protein patterns. The model achieved high accuracy in predicting tissues (98%) and cell types (99%) based on protein abundance. The results provide valuable insights into tissue-specific proteins and can be applied to various downstream applications.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Andreia Ferreira, Evy Timmerman, An Staes, Marnik Vuylsteke, Louis De Muynck, Kris Gevaert
Summary: By using affinity-enrichment mass spectrometry, we identified novel potential protein ligands that may interact with (3S-)HS. Our dataset expands the repertoire of proteins that depend on 3S-HS in (patho)physiological conditions, providing new insights into the molecular mechanisms involved.
Article
Biochemical Research Methods
Pieter Verschaffelt, Alessandro Tanca, Marcello Abbondio, Tim van den Bossche, Tibo Vande Moortele, Peter Dawyndt, Lennart Martens, Bart Mesuere
Summary: Unipept Desktop 2.0 is the latest version of the Unipept Desktop tool, which now supports the analysis of metaproteogenomics datasets. It allows for the automatic construction of targeted protein reference databases for improved taxonomic and functional resolution. By limiting the proteins in the database, (meta)proteogenomic analyses can also be performed with better control and privacy. A case study using human gut metaproteome dataset and matched 16S rRNA gene sequencing data is presented as a proof of concept.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Fan Xu, Ruoyao Li, Erika D. von Gromoff, Bettina Knapp, Friedel Drepper, Bettina Warscheid, Ralf Baumeister, Wenjing Qi
Summary: Xu and colleagues found that the endoribonuclease ENDU-2/ENDOU activates transcriptional reprogramming after brief heat shock, leading to long-term beneficial effects in C. elegans.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Tine Claeys, Tim van den Bossche, Yasset Perez-Riverol, Kris Gevaert, Juan Antonio Vizcaino, Lennart Martens
Summary: Public proteomics data often lack essential metadata, but lesSDRF provides a tool to simplify the process of metadata annotation and ensure that the data has lasting impact beyond its initial publication.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Florian Becker, Simon Fuchs, Lukas Refisch, Friedel Drepper, Wolfgang Bildl, Uwe Schulte, Shuo Liang, Jonas Immanuel Heinicke, Sierra C. Hansen, Clemens Kreutz, Bettina Warscheid, Bernd Fakler, Evgeny Mymrikov, Carola Hunte
Summary: This study reveals that calcium binding and myristoylation independently affect the conformation and functions of human CHP3. Calcium binding increases the flexibility and hydrophobicity of CHP3, indicating an open conformation. Myristoylation enhances the flexibility of CHP3 and decreases its affinity to NHE1 independently of the bound ion.
Article
Biology
Markus Gerber, Ida Suppanz, Silke Oeljeklaus, Moritz Niemann, Sandro Kaser, Bettina Warscheid, Andre Schneider, Caroline E. Dewar
Summary: The AAA-ATPase Msp1 is involved in extracting mislocalized outer membrane proteins and maintaining mitochondrial proteostasis. It localizes to glycosomes and the mitochondrial outer membrane, where it forms a complex with four outer membrane proteins. The trypanosome-specific pATOM36 mediates the assembly of this complex and is required for efficient proteasomal digestion of unassembled substrates.
LIFE SCIENCE ALLIANCE
(2023)
Article
Endocrinology & Metabolism
Sukanya Guhathakurta, Niyazi Umut Erdogdu, Juliane J. Hoffmann, Iga Grzadzielewska, Alexander Schendzielorz, Janine Seyfferth, Christoph U. Martensson, Mauro Corrado, Adam Karoutas, Bettina Warscheid, Nikolaus Pfanner, Thomas Becker, Asifa Akhtar
Summary: This study reveals the important role of MYST family lysine acetyltransferase MOF in energy metabolism through mitochondrial protein acetylation. Loss of MOF-KANSL complex members leads to mitochondrial defects, and COX17 is identified as a target of MOF acetylation. Acetylation-mimetic COX17 can rescue mitochondrial defects, suggesting an activatory role of mitochondrial protein acetylation in the electron transport chain. The findings from patients with MOF syndrome also support these conclusions.
Article
Biochemical Research Methods
Ralf Gabriels, Arthur Declercq, Robbin Bouwmeester, Sven Degroeve, Lennart Martens
Summary: This study introduces a Python package called psm_utils, which can read and write various proteomics search engine output file formats and handle peptide-spectrum matches (PSMs) and PSM lists in a unified data structure. The package includes a Python API and command line interface, as well as a user-friendly web application for converting PSM files and retrieving basic PSM statistics.
JOURNAL OF PROTEOME RESEARCH
(2023)