Article
Biochemical Research Methods
Andrea M. Brunner, Philip Lossl, Paul P. Geurink, Huib Ovaa, P. Albanese, A. F. Maarten Altelaar, Albert J. R. Heck, Richard A. Scheltema
Summary: Top-down proteomics combined with bioinformatics approaches can improve the localization and quantification of protein modifications, even for positional isomers with the same number of modifications at different sites. This method shows promising results in characterizing multiple modified proteins and estimating the stoichiometry of phosphorylated sites.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Biochemical Research Methods
Lana Abou Zeid, Albert Pell, Theo Tytus, Pascale Delangle, Carole Bresson
Summary: This study utilized HILIC-ESI-MS to separate multiphosphorylated cyclic peptides and their positional isomers, evaluating the selectivity of HILIC columns and the impact of mobile phase on separation selectivity. It explored the retention mechanism of different peptides, finding that the classic hydrophilic partitioning mechanism was followed exclusively on amide and diol columns. The research also revealed that the position of phosphorylated amino acids in the peptide backbone had an impact on retention, enabling the separation of positional isomers using HILIC.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Jia-Xing Fu, Yong Liu, Liang-Hui Chen, Wang-Kang Han, Xin Liu, Jun-Xiang Shao, Xiaodong Yan, Zhi-Guo Gu
Summary: Humidity is a crucial factor influencing human health. Researchers have developed positional isomers, p-COF and o-COF, as covalent organic frameworks for indoor humidity regulation. Although they have the same topology and pore size, p-COF and o-COF exhibit different water adsorption behaviors due to subtle differences in adsorption sites. Especially, o-COF shows a steep adsorption isotherm and hysteresis loop at 45-65% RH, making it perfectly suitable for indoor humidity regulation. Lab experiments demonstrate that o-COF can control room humidity within the range of 45-60% RH when external environment humidity is 20-75% RH. o-COF has great potential as a dual humidification/dehumidification adsorbent for indoor humidity regulation.
Article
Biochemical Research Methods
Peng Che, J. Tyler Davidson, Kristina Still, Jeroen Kool, Isabelle Kohler
Summary: Synthetic cathinones, including 3-MMC, pose a serious threat to public health and their metabolism remains largely unknown. In this study, the metabolism of 2-MMC, 3-MMC, and 4-MMC was investigated using both male and female rat and human liver microsomal incubations. A total of 25 phase I metabolites of MMCs were detected, with seven sex-specific metabolites found exclusively in male rat liver microsomal incubations. Differences in relative abundance were observed between male and female rat liver microsomes, but no sex-specific metabolites or significant differences were observed in human liver microsomal incubations.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Andrew J. Tague, Papanin Putsathit, Thomas Riley, Paul A. Keller, Stephen G. Pyne
Summary: Small-molecule antimicrobial peptidomimetic amphiphiles show promise as novel antimicrobials, with spatial positioning of key hydrophobic and hydrophilic groups playing a significant role in antimicrobial efficacy and selectivity. Positional isomers of the lead biphenyl antimicrobial peptidomimetic compound exhibited varied efficacy against different pathogens, with changes in molecular shape impacting Gram-negative antibacterial efficacy.
ACS MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Yuxin Liu, Peter H. Seeberger, Nabyl Merbouh, Felix F. Loeffler
Summary: This study constructed reversible multichannel fluorescent devices using two fluorescent positional isomers, improving the reliability of information encryption. The two isomers showed different fluorescence colors in an acidic environment, allowing for stepwise encryption of information.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Jean-David Peltier, Benoit Heinrich, Bertrand Donnio, Olzhas A. Ibraikulov, Thomas Heiser, Nicolas Leclerc, Joelle Rault-Berthelot, Cyril Poriel
Summary: The influence of positional isomerism on the properties of dispiroacridine-indacenobisthiophene molecules and their charge transport properties is significant, with higher charge transport mobility values observed in the meta isomer compared to the para isomer. This finding highlights the key role played by the spiro-connected fragments in these molecular systems.
MATERIALS CHEMISTRY FRONTIERS
(2022)
Article
Biochemical Research Methods
Johan Lillja, Ingela Lanekoff
Summary: Glycerophospholipids are essential for life, and the different acyl chain connectivity to the glycerol backbone has significant effects on biological function. Analytical techniques are needed to identify and quantify these different connectivity patterns in complex biological samples. In this study, the researchers used a combination of silver ion cationization and mass spectrometry to identify isomers of phosphatidylcholine species, and they found differences in concentration and localization patterns among these isomers.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Jiajun Wang, Jigneshkumar Dahyabhai Prajapati, Fan Gao, Yi-Lun Ying, Ulrich Kleinekathoefer, Mathias Winterhalter, Yi-Tao Long
Summary: Chirality is important but often overlooked in biological and chemical processes due to technical limitations. Researchers have used an electrostatically asymmetric membrane channel to successfully identify chiral amino acids in single peptides. This study provides a new approach for developing chiral recognition and protein sequencing methods.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Applied
Rafael Garces, Enrique Martinez-Force, Monica Venegas-Caleron, Antonio J. Moreno-Perez, Joaquin J. Salas
Summary: The properties of Triacylglycerols (TAGs) depend on their fatty acid composition and distribution. The presence of saturated fatty acids at different positions of TAGs is important in determining the melting and tempering profile of many solid and plastic fats. We developed a GC/MS based method to determine the composition of positional isomers of disaturated TAGs involved in food formulations, which does not require prior purification of the TAG species. This method allows for rapid determination of the regioisomer distribution of major TAG species in a crude fat, facilitating the characterization of various fats, oils, and butter in food formulations.
Review
Chemistry, Analytical
Maartje Verhoeven, Jennifer Bonetti, Ruben Kranenburg, Arian van Asten
Summary: Due to the increasing number of NPSs, identifying drug isomers is becoming more challenging for forensic laboratories. Currently, GC-MS is the standard technique, but it cannot confidently differentiate positional isomers. This review provides an overview of methods for differentiating and identifying NPS positional isomers and proposes a workflow for routine analysis in forensic laboratories.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Oznur Yeni, Amira Gharbi, Stephane Chambert, Jean Rouillon, Abdul-Rahman Allouche, Baptiste Schindler, Isabelle Compagnon
Summary: The study utilized infrared ion spectroscopy and ab initio calculations to assess the structure of O-acetylated monosaccharide ions in the gas phase of a mass analyzer. Experimental results demonstrate that the position of O-acetyl groups is retained through the transfer from solution to the gas phase and can be identified by IRMPD spectroscopy.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Analytical
Irina Dyukova, Ahmed Ben Faleh, Stephan Warnke, Natalia Yalovenko, Vasyl Yatsyna, Priyanka Bansal, Thomas R. Rizzo
Summary: Glycosylation patterns in monoclonal antibodies can vary significantly between different host cell types, affecting the safety, efficacy, and immunogenicity of the antibodies. This study demonstrates the potential of high-resolution ion mobility combined with cryogenic infrared spectroscopy in distinguishing isomeric glycans with different terminal galactose positions, which is critical for ensuring antibody quality. Additionally, the impact of host cell lines on the IgG G1F glycan profile at the isomer level was illustrated in this work.
Article
Materials Science, Multidisciplinary
Clement Brouillac, Fan-Cheng Kong, Joelle Rault-Berthelot, Cassandre Quinton, Zuo-Quan Jiang, Cyril Poriel
Summary: Designing deep-blue fluorophores with a low CIEy is crucial for OLED technology, whether for display applications or new applications like antibacterial light sources. This study reports the synthesis, physico-chemical properties, and application of two deep-blue emitters in an OLED. The emitters demonstrated high device performance with suitable CIE coordinates, and one emitter showed a deep-blue emission with an EQE of 1.7% and a V-on of 4 V, fitting the NTSC and EBU standards.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Chemistry, Analytical
Fangling Wu, Liancheng Gu, Xinhua Dai, Shutong Yang, Fuxing Xu, Xiang Fang, Shaoning Yu, Chuan-Fan Ding
Summary: Positional isomer recognition is a challenging scientific issue, and the simultaneous recognition of ABSA isomers using TIMS-TOF-MS was achieved by measuring different ion mobility or spatial conformations. The study also demonstrated a method for relative quantification of the isomers with good linearity and precision at different molar ratios.
Review
Biochemical Research Methods
Lindsay K. Pino, Seth C. Just, Michael J. MacCoss, Brian C. Searle
MOLECULAR & CELLULAR PROTEOMICS
(2020)
Article
Multidisciplinary Sciences
Brian C. Searle, Kristian E. Swearingen, Christopher A. Barnes, Tobias Schmidt, Siegfried Gessulat, Bernhard Kuester, Mathias Wilhelm
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Aaron E. Robinson, Aleksandra Binek, Vidya Venkatraman, Brian C. Searle, Ronald J. Holewinski, George Rosenberger, Sarah J. Parker, Nathan Basisty, Xueshu Xie, Peder J. Lund, Gautam Saxena, Jose M. Mato, Benjamin A. Garcia, Birgit Schilling, Shelly C. Lu, Jennifer E. Van Eyk
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Biochemical Research Methods
Damien B. Wilburn, Alicia L. Richards, Danielle L. Swaney, Brian C. Searle
Summary: Library searching is a powerful technique for detecting peptides, and the authors have developed a software tool CIDer to convert libraries between HCD and CID fragmentation methods. Using simple linear models and basic principles of peptide fragmentation, they can explain up to 43% of the variation between ions fragmented by HCD and CID. They also found that in some cases, searching converted CID libraries can detect more peptides.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
America Vera-Montecinos, Ricard Rodriguez-Mias, Karina S. MacDowell, Borja Garcia-Bueno, Alvaro G. Bris, Javier R. Caso, Judit Villen, Belen Ramos
Summary: The study identified altered stress- and mitochondrial disease-related proteins in the cerebellum of schizophrenia patients, suggesting potential novel targets for therapeutic interventions. These findings indicate a dysregulation in energy, immune, and axonal networks, with METTL7A identified as a possible relevant altered stress-related protein in this context.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Biochemical Research Methods
Ian R. Smith, Kyle N. Hess, Anna A. Bakhtina, Anthony S. Valente, Ricard A. Rodriguez-Mias, Judit Villen
Article
Virology
Brian McEllin, Brian C. Searle, Lisa DePledge, George Sun, Charles Cobbs, Mohsen Karimi
Summary: HPV-positive head and neck squamous cell carcinoma (HNSCC) can metastasize to rare sites such as the brain, with specific risk factors for this phenotype needing further study. Analysis of tumors from two patients revealed HPV genome integration into host genome at known hotspots, providing potential targets for future research on biomarkers for metastasis prediction and novel therapeutic options.
Article
Geriatrics & Gerontology
Matt Kaeberlein, Alessandro Bitto, Maitreya J. Dunham, Warren Ladiges, Su-In Lee, Michael J. MacCoss, Alexander Mendenhall, Daniel E. L. Promislow, Peter S. Rabinovitch, Judit Villen, Lu Wang, Yuliang Wang, Jessica E. Young
Summary: The University of Washington Nathan Shock Center of Excellence provides leadership and resources for the geroscience community, supporting aging-related studies, organizing seminars and training programs, and partnering with other institutions for strategic initiatives.
Article
Biochemical Research Methods
Matthew D. Berg, Joshua R. Isaacson, Ecaterina Cozma, Julie Genereaux, Patrick Lajoie, Judit Villen, Christopher J. Brandl
Summary: Research has shown that tRNA expression can be inversely regulated by controlling the expression of adjacent RNAP II promoters. This is crucial for achieving high levels of novel protein expression. In Saccharomyces cerevisiae, introducing an inducible tRNA system allows the study of the proteotoxic effects of mistranslation on cells, with high levels of mistranslation causing cells to arrest in the G1 phase and altering cell morphology.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Genetics & Heredity
Joshua R. Isaacson, Matthew D. Berg, Brendan Charles, Jessica Jagiello, Judit Villen, Christopher J. Brandl, Amanda J. Moehring
Summary: This study integrated a mistranslating transfer RNA variant into the genome of Drosophila melanogaster, resulting in extended development time, decreased adult fly count, morphological deformities, and poor climbing performance. These effects were more pronounced in female flies and worsened with age. This model provides insights into the synergistic effects of mistranslating transfer RNA variants and disease-causing alleles.
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
Matthew D. Berg, Yanrui Zhu, Raphael Loll-Krippleber, Bryan-Joseph San Luis, Julie Genereaux, Charles Boone, Judit Villen, Grant W. Brown, Christopher J. Brandl
Summary: This study investigates the genetic interactions between a gene encoding mistranslating tRNA and other genes in yeast. The results show that the frequency of mistranslation correlates with the impact on cell growth, and the extent of the genetic interaction varies depending on the genetic background. These findings have important implications for understanding the effects of tRNA variants on disease and highlight the need to consider both the individual's genetic background and the expression of the mistranslating tRNA variant.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemical Research Methods
Alexander Hogrebe, Kyle N. Hess, Ariadna Llovet, Y. Julian Ramos, Anthony S. Barente, Daniel Hernandez-Portugues, Ian R. Smith, Ricard A. Rodriguez-Mias, Judit Villen
Summary: The study introduces IsobaricQuant, an open-source software tool for the quantification, visualization, and filtering of labeled peptides. IsobaricQuant improves quantitative accuracy and filters scans with inaccurate quantification using quality control scores, reducing protein variability.
Article
Chemistry, Analytical
Ian R. Smith, Jimmy K. Eng, Anthony S. Barente, Alexander Hogrebe, Ariadna Llovet, Ricard A. Rodriguez-Mias, Judit Villen
Summary: Stable-isotope labeling with amino acids in cell culture (SILAC)-based metabolic labeling is a widely used proteomics approach for quantitative comparisons. In this study, a new strategy was developed to coisolate and fragment SILAC peptide pairs for relative quantification. The modified database search engine and developed tool facilitated the analysis and quantification of SILAC peptide pairs. The coisolation approach improved the expectation scores and achieved more quantifications compared to traditional methods.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Anthony S. Barente, Judit Villen
Summary: Determining the correct localization of post-translational modifications (PTMs) on peptides is crucial for interpreting their impact on protein function. PyAscore, an efficient and versatile Python implementation of the Ascore algorithm, allows for scoring the localization of user-defined PTMs in data-dependent mass spectrometry.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Alexis Chang, Mario Leutert, Ricard A. Rodriguez-Mias, Judit Villen
Summary: Phosphotyrosine (pY) enrichment is critical for understanding cellular signaling through mass spectrometry-based proteomics. However, current methods are expensive and not highly reproducible. We present a new method called R2-pY that can handle multiple samples in parallel, has high reproducibility, and produces comprehensive proteomic and phosphoproteomic samples. R2-pY extends our previous proteomic sample preparation framework and allows for large-scale studies of pY signaling.
JOURNAL OF PROTEOME RESEARCH
(2023)
