Article
Biochemical Research Methods
Xinyue Liu, Valentina Rossio, Sanjukta Guha Thakurta, Amarjeet Flora, Leigh Foster, Ryan D. Bomgarden, Steven P. Gygi, Joao A. Paulo
Summary: Protein phosphorylation is a central mechanism of cellular signal transduction. This study compares two phosphopeptide enrichment methods and finds that magnetic beads can seamlessly substitute spin columns for global phosphoproteome profiling. The scalable and automation-friendly magnetic bead-based workflow is an equivalent and more flexible enrichment strategy.
JOURNAL OF PROTEOMICS
(2022)
Review
Chemistry, Analytical
Ruizhi Tang, Quan Bai, Shujuan Ma, Junjie Ou
Summary: In the last decade, immobilized metal ion chromatography (IMAC) has made significant advances in phosphoproteomic profiling. IMAC enrichment strategy captures phosphopeptides through chemical interaction with immobilized metal cations. The design of IMAC enrichment materials and workflows is crucial for phosphoproteomic profiling.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Huimin Chu, Haoyang Zheng, Aizhu Miao, Chunhui Deng, Nianrong Sun
Summary: This study used hybrid metal organic frameworks (HMOFs) to investigate the region-resolved phosphoproteome of the human lens, identifying phosphosites and phosphoproteins in the capsule, cortex, and nucleus. This provided a relatively extensive distribution map of phosphorylation in the human lens for the first time.
CHINESE CHEMICAL LETTERS
(2023)
Article
Chemistry, Applied
Wenrui Wu, Ruizhi Tang, Zhouxian Li, Yehua Shen, Shujuan Ma, Junjie Ou
Summary: A Ti4+-immobilized polydispersed phosphate-rich microsphere was successfully fabricated using inverse suspension polymerization method, showing excellent sensitivity, selectivity, and adsorption capacity. This method requires only two steps to synthesize Ti4+-IMAC, offering a simpler and more efficient approach for protein phosphorylation research and potential for pilot production and commercialization.
Article
Nanoscience & Nanotechnology
Sen Zhang, Jia-yuan Li, Wei Gao, Jun-qin Qiao, Hong-zhen Lian
Summary: Ti3C2-Fe3O4 composites with exposed non-modified Ti3C2 MXene nanosheets were designed and prepared for the enrichment of phosphopeptides. The composites interacted with the phosphopeptides through metal oxide affinity chromatography and hydrophilic interaction chromatography mechanisms. The magnetic nanomaterial showed high sensitivity and selectivity, and satisfactory results were obtained in the enrichment of phosphopeptides from real samples and traditional Chinese medicine injection.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Nanoscience & Nanotechnology
Hong-zhen Lian, Sen Zhang, Jia-yuan Li, Wei Gao, Jun-qin Qiao
Summary: Ti3C2-Fe3O4 composites with exposed non-modified Ti3C2 MXene nanosheets were prepared and used for the enrichment of phosphopeptides. The composites interacted with phosphopeptides through metal oxide affinity chromatography mechanism and hydrophilic interaction chromatography mechanism. The magnetic nanomaterial showed high sensitivity and selectivity towards phosphopeptides and was successfully applied in real samples and complex matrices.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Physical
C. Bhagya Lakshmi, S. Jeya Lakshmi, Jeyanthinath Mayandi, S. Anna Venus, R. Marnadu, X. Vasanth Winston, M. Aslam Manthrammel, Mohd. Shkir
Summary: CuBiSe/metal oxide (TiO2, V2O5, and ZnO) nanocomposites were synthesized using a simple and low-cost hydrothermal technique for Dye-Sensitised Solar Cells (DSSCs) application. Various analyses including XRD, XPS, SEM with EDX, FTIR, UV-Visible Spectroscopy, PL spectrum, Hall Effect analysis, and Impedance analysis were performed to evaluate the nanocomposites. The photovoltaic performance of DSSCs with CBS/TiO2, CBS/V2O5, and CBS/ZnO photoanodes was investigated. The CBS/V2O5 DSSCs device demonstrated a short-circuit photocurrent density of 3.728 mA cm2, an open circuit voltage of 0.398 V, a fill factor of 0.72, and a power conversion efficiency (PCE) of 1.07%, higher than that of DSSCs using CBS/TiO2 and CBS/ZnO photoanodes (PCE = 0.62 and 0.37%). These results suggest that the prepared nanocomposite is a suitable photoanodic material for DSSCs applications.
SURFACES AND INTERFACES
(2023)
Article
Chemistry, Analytical
Qianying Sheng, Chenli Xue, Yang Zhou, Junyan Li, Huihui Yuan, Yanxiong Ke, Minbo Lan
Summary: The study demonstrated the selective enrichment of glycopeptides and phosphopeptides through the preparation of Al3+-doping-TiO2 mixed oxide microspheres, leading to significantly improved signal-to-noise ratio in the samples of human serum immunoglobulin G (IgG) and alpha-casein. This method provides a novel insight for post-translational modification proteomics research.
Article
Materials Science, Biomaterials
Dandan Jiang, Siyu Wu, Yangyang Li, Ruixue Qi, Jinghai Liu
Summary: In this study, magnetic polyoxometalate-based metal-organic frameworks were designed and used for phosphopeptide enrichment. The material exhibited strong affinity and selectivity for phosphopeptides, and coupled with mass spectrometry detection, achieved high sensitivity and reusability, showing great potential for practical application in phosphopeptide detection.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2023)
Article
Astronomy & Astrophysics
Maria Emilia De Rossi, Volker Bromm
Summary: By implementing a model of primordial dust emission, the study predicts dust-continuum fluxes for massive galaxy sources detected by the James Webb Space Telescope (JWST) at high redshift. The findings suggest that the low dust-to-metal mass ratio and metallicity values are in agreement with some proposed scenarios to explain the non-detection of FIR dust continuum for high-z JWST galaxy candidates. ALMA observations could further constrain the dust chemistry and distribution in the early universe.
ASTROPHYSICAL JOURNAL LETTERS
(2023)
Article
Thermodynamics
Jennifer L. Gottfried, Elliot R. Wainwright, Sidi Huang, Yue Jiang, Xiaolin Zheng
Summary: Boron is a promising fuel for energetic materials due to its high energy density when combined with CuO and Bi2O3 in thermite reactions. The application of LASEM technique has enabled the quantification of energy release and excitation temperatures of B/metal oxide samples on microsecond and millisecond timescales. The enhancement of ignition in these composites contributes to the early-time energy release, as shown by relative measurements in agreement with bomb calorimetry and DSC analysis. Additionally, the strong affinity of CuO for both B and Bi2O3 leads to a synergetic enhancement effect in the binary metal oxide mixture.
COMBUSTION AND FLAME
(2021)
Article
Engineering, Environmental
Zhengchen Wu, Chen Jin, Ziqi Yang, Xiang Qian, Renchao Che
Summary: Researchers have developed a high-yield and green method for synthesizing hierarchically ultra-vesicular microspheres. The method involves creating numerous multi-sized bubbles inside the microspheres, which enhances the dielectric loss capacity and impedance matching of microwave absorption materials. The results show that the ultra-vesicular microspheres of SnO2 and Co demonstrate excellent absorption performance across the frequency range of 2 to 18 GHz.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Engineering, Environmental
Yonghai Zhang, Hongqiang Chen, Xiong Zhao, Xiang Ma, Lei Huang, Yinan Qiu, Jinjia Wei, Nanjing Hao
Summary: This paper introduces a robust acoustofluidic bubble-driven micromixer for the controllable synthesis of functional nano-array inside a glass capillary, which exhibits efficient photodegradation and metal ion enrichment. The morphology, density, and size of the nano-array can be precisely adjusted by reactant type, seeding phase, and reaction time. The ZnO nanorod array shows superior degradation efficiency and Cu2+ enrichment performance.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biochemical Research Methods
Kaina Zhang, Yun Hao, Dehua Hu, Suimin Deng, Yuhao Jin, Xiangfeng Wang, Hailing Liu, Yuan Liu, Mengxia Xie
Summary: A hydrophilic metal-organic network based on Ti4+ and dual natural ligand, tannic acid (TA) and phytic acid (PA), has been developed for enriching phosphopeptides from complex bio-samples before liquid chromatography-mass spectrometric analysis. The sorbent, TA-Ti-PA@Fe3O4, exhibited satisfactory selectivity and high adsorption capacity for phosphopeptides, showing great potential in phosphoproteome research.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Chemistry, Analytical
Sheng Bi, Xue Yang, Baoyue Zhang, Yukui Tong, Feng Zhang, Miaomiao Tian
Summary: In this study, ZIF-based metal oxide molecularly imprinted polymers (ZIF@PEI@TiO2-MIPs) were used for efficient and selective separation and enrichment of ovalbumin in egg white samples. The adsorbent demonstrated good selectivity, adsorption performance, and stability, making it a promising tool for the identification of ovalbumin in complex samples.
MICROCHEMICAL JOURNAL
(2022)
Article
Oncology
Lukas Leiendecker, Tobias Neumann, Pauline S. Jung, Shona M. Cronin, Thomas L. Steinacker, Alexander Schleiffer, Michael Schutzbier, Karl Mechtler, Thibault Kervarrec, Estelle Laurent, Kamel Bachiri, Etienne Coyaud, Rajmohan Murali, Klaus J. Busam, Babak Itzinger-Monshi, Reinhard Kirnbauer, Lorenzo Cerroni, Eduardo Calonje, Arno Rutten, Frank Stubenrauch, Klaus G. Griewank, Thomas Wiesner, Anna C. Obenauf
Summary: This study reveals the presence of human papillomavirus 42 (HPV42) in 96% of digital papillary adenocarcinoma (DPA), a cancer occurring on fingers and toes. It shows that HPV42, previously considered nononcogenic, behaves similarly to oncogenic, high-risk HPVs. Machine learning analysis indicates that HPV-driven transformation induces a germ cell-like transcriptional program conserved across all HPV-driven cancers, with implications for early detection, diagnosis, and therapy.
Article
Biochemical Research Methods
Sebastian Dorl, Stephan Winkler, Karl Mechtler, Viktoria Dorfer
Summary: Spectral library search enables more sensitive peptide identification in tandem mass spectrometry experiments, but suffers from limited availability of high-quality libraries and the difficulty of creating decoy spectra for result validation. MS Ana is a new spectral library search engine that addresses these issues by allowing the use of curated or predicted libraries and providing robust false discovery control through its own decoy library generation algorithm. In benchmark tests, MS Ana outperformed database search, achieving 36% more spectrum matches and 4% more proteins identified in single-shot human cell-line data. The quality of result validation was demonstrated through tests on synthetic peptide pools, and the importance of library selection was highlighted by comparing the performance of different publicly available human spectral libraries.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Friederike Leesch, Laura Lorenzo-Orts, Carina Pribitzer, Irina Grishkovskaya, Josef Roehsner, Anastasia Chugunova, Manuel Matzinger, Elisabeth Roitinger, Katarina Belacic, Susanne Kandolf, Tzi-Yang Lin, Karl Mechtler, Anton Meinhart, David Haselbach, Andrea Pauli
Summary: Using mass spectrometry and cryo-electron microscopy, the study provides molecular evidence that ribosomes transition from a dormant state to an active state during early embryogenesis. Dormant ribosomes are associated with four conserved factors that stabilize ribosomes and repress translation. Addition of recombinant zebrafish Dap1b protein can block translation and reconstitute the dormant ribosome state in vitro.
Article
Chemistry, Analytical
Manuel Matzinger, Elisabeth Mueller, Gerhard Duernberger, Peter Pichler, Karl Mechtler
Summary: We report a comprehensive workflow that includes improved strategies for all steps, from cell lysis to data analysis. The workflow is easy to implement even for novice users, thanks to the use of convenient-to-handle 1 μL sample volume and standardized 384-well plates. Using advanced micro-pillar columns, ultrashort gradient lengths down to 5 minutes were tested for high throughput. By benchmarking different acquisition methods and data analysis algorithms, the workflow achieved identification of 1790 proteins in a single cell using data-dependent acquisition (DDA), and more than 2200 proteins from single-cell level input using data-independent acquisition (DIA) in a 20-minute active gradient. The workflow also demonstrated its suitability for differentiating two cell lines, indicating its potential for cellular heterogeneity determination.
ANALYTICAL CHEMISTRY
(2023)
Article
Oncology
Ossia M. Eichhoff, Corinne I. Stoffel, Jan Kasler, Luzia Briker, Patrick Turko, Gergely Karsai, Nina Zila, Verena Paulitschke, Phil F. Cheng, Alexander Leitner, Andrea Bileck, Nicola Zamboni, Anja Irmisch, Zsolt Balazs, Aizhan Tastanova, Susana Pascoal, Pal Johansen, Rebekka Wegmann, Julien Mena, Alaa Othman, Vasanthi S. Viswanathan, Judith Wenzina, Andrea Aloia, Annalisa Saltari, Andreas Dzung, Michael Krauthammer, Stuart L. Schreiber, Thorsten Hornemann, Martin Distel, Berend Snijder, Reinhard Dummer, Mitchell P. Levesque
Summary: The clinical management of NRAS-mutated melanomas is challenging due to resistance that arises through genetic, transcriptional, and metabolic adaptation. However, the adoption of a mesenchymal phenotype with a quiescent metabolic program in NRAS-mutated melanoma cells confers sensitivity to reactive oxygen species (ROS) induction, which can be inhibited by ROS inducers in combination with MAPK pathway inhibitors. The findings suggest that targeting both metabolic reprogramming and MAPK signaling could improve patient treatment in melanoma and other cancers.
Article
Biochemistry & Molecular Biology
Leonid Serebreni, Lisa-Marie Pleyer, Vanja Haberle, Oliver Hendy, Anna Vlasova, Vincent Loubiere, Filip Nemcko, Katharina Bergauer, Elisabeth Roitinger, Karl Mechtler, Alexander Stark
Summary: Different classes of promoters have distinct mechanisms of transcription initiation, resulting in either focused or dispersed initiation patterns.
Review
Biochemistry & Molecular Biology
Benjamin Steinmetz, Izabela Smok, Maria Bikaki, Alexander Leitner
Summary: Understanding how proteins and RNAs form complexes and affect each other is crucial for studying cellular processes and drug discovery. Mass spectrometry and classical structural biology techniques provide high-resolution and detailed structural information, which are important for investigating protein-RNA interactions.
ESSAYS IN BIOCHEMISTRY
(2023)
Review
Biochemical Research Methods
Manuel Matzinger, Rupert L. Mayer, Karl Mechtler
Summary: Mapping proteomic fingerprints to transcriptomic data is crucial for understanding gene expression and phenotype. Despite challenges in protein amplification and lack of established gold standard workflows, advances in microfluidics, sample separation, data acquisition, and analysis have improved the analysis of tiny sample amounts. Sensitivity, robustness, and throughput are still urgent needs, and label-free single-cell mass spectrometry is a promising strategy for unbiased quantification. This review focuses on recent advances in label-free single-cell mass spectrometry workflows and provides guidance for method selection and future prospects.
Article
Multidisciplinary Sciences
Andreas Lackner, Michael Mueller, Magdalena Gamperl, Delyana Stoeva, Olivia Langmann, Henrieta Papuchova, Elisabeth Roitinger, Gerhard Duernberger, Richard Imre, Karl Mechtler, Paulina A. A. Latos
Summary: The Erf-NCoR1/2 complex controls trophoblast differentiation by linking signalling with transcriptional repression.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Jaydeep Sidhaye, Philipp Trepte, Natalie Sepke, Maria Novatchkova, Michael Schutzbier, Gerhard Duernberger, Karl Mechtler, Juergen A. Knoblich
Summary: By analyzing the transcriptome and epigenome during human corticogenesis, important gene regulatory networks have been identified. Through the use of human brain organoids, specific transcriptome and proteome analyses were conducted, revealing gene expression modules during cortical development. One module involving mTOR-mediated regulation of translation was investigated, showing that partial inhibition of ribosomal genes translation prevents premature translation of differentiation markers, crucial for maintaining the accuracy of cortical development.
Article
Materials Science, Multidisciplinary
Saara Sirkia, Syeda Qudsia, Minna Siekkinen, Wolfgang Hoepfl, Tanja Budde, Jan-Henrik Smatt, Jouko Peltonen, Leena Hupa, Terhi J. Heino, Pekka K. Vallittu
Summary: This study aimed to characterize the physicochemical and biological properties of functionalized calcium carbonate (FCC) consisting of calcium carbonate particles with a hydroxyapatite layer. The results showed that FCC could adsorb calcium ions from the surrounding liquid, which should be carefully considered in cell culture assays.
Article
Biochemical Research Methods
Micha J. J. Birklbauer, Manuel Matzinger, Fraenze Mueller, Karl Mechtler, Viktoria Dorfer
Summary: In the paper "Cross-linking Mass Spectrometry 2.0", the authors present an updated version of the MS Annika search engine, which accurately identifies cross-linked peptides and introduces a novel scoring function. The evaluation shows that MS Annika 2.0 outperforms other search engines in terms of true unique cross-link detection and false discovery rate estimation.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Chris P. Sarnowski, Michael Gotze, Alexander Leitner
Summary: Cross-linking and mass spectrometry (XL-MS) workflows and the recently developed cross-linking of isotope-labeled RNA and mass spectrometry (CLIR-MS) approach are important for analyzing protein-protein and protein-RNA interactions. RNxQuest is a Python package extension for xQuest that automates the analysis approach required for CLIR-MS data, providing state-of-the-art processing and visualization functionality.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jann-Louis Hau, Susann Kaltwasser, Valentin Muras, Marco S. Casutt, Georg Vohl, Bjoern Claussen, Wojtek Steffen, Alexander Leitner, Eckhard Bill, George E. Cutsail, Serena Debeer, Janet Vonck, Julia Steuber, Guenter Fritz
Summary: This study reveals that ion pumping in Na+-NQR is driven by large conformational changes coupling electron transfer to ion translocation. This mechanism is of significant importance for NADH oxidation in the human pathogen Vibrio cholerae.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Friederike Leesch, Laura Lorenzo-Orts, Carina Pribitzer, Irina Grishkovskaya, Josef Roehsner, Anastasia Chugunova, Manuel Matzinger, Elisabeth Roitinger, Katarina Belacic, Susanne Kandolf, Tzi-Yang Lin, Karl Mechtler, Anton Meinhart, David Haselbach, Andrea Pauli
Summary: Using mass spectrometry and cryo-electron microscopy analyses, we show that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis in zebrafish and Xenopus laevis. Dormant ribosomes are associated with conserved factors that form two modules, responsible for stabilizing ribosomes and repressing translation. A newly discovered translational inhibitor, Dap1b, is found to play a key role in maintaining the dormant state of ribosomes.
