Article
Chemistry, Analytical
Tarang Jadav, Pinaki Sengupta
Summary: In this study, an Excel-based ProteoExcel(TP) tool was developed for the quick and accurate selection of surrogate peptides for the entire protein family. The tool is highly user-friendly and flexible, which can significantly reduce the workload and increase efficiency for scientists working in proteomics research.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2023)
Article
Food Science & Technology
Zhiyuan Huang, Wenming Dong, Jiangping Fan, Yang Tian, Aixiang Huang, Xuefeng Wang
Summary: Our study investigated the antimicrobial mechanism of the peptide MOp2 from Moringa oleifera seeds against Staphylococcus aureus using TMT-based proteomics technology. We identified differentially expressed proteins involved in inositol phosphate metabolism, cell wall synthesis, and energy metabolism, which resulted in membrane damage, oxidative stress, and cell death in S. aureus. Molecular docking further showed that MOp2 interacted with multiple proteins, confirming its multi-targeted mechanism. These findings provide a theoretical basis for the application of MOp2 as a novel food preservative and antibiotic substitute.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Biochemical Research Methods
Sang-Yeop Lee, Hayoung Lee, Sung Ho Yun, Edmond Changkyun Park, Giwan Seo, Hye-Yeon Kim, Sangmi Jun, Nam Hoon Kim, Dongseob Tark, Ju Yeon Lee, Chang-Seop Lee, Seung Il Kim
Summary: Proteomic analysis revealed that the nucleocapsid (N) protein is the major antigen protein in the serum of severe fever with thrombocytopenia syndrome (SFTS) patients, and the N-terminal tryptic peptide of the N protein might be a useful proteomic target for direct detection of SFTS virus.
CLINICAL PROTEOMICS
(2022)
Article
Multidisciplinary Sciences
Rodolfo Ciuffa, Federico Uliana, Jonathan Mannion, Martin Mehnert, Tencho Tenev, Cathy Marulli, Ari Satanowski, Lena Maria Leone Keller, Pilar Natalia Rodilla Ramirez, Alessandro Ori, Matthias Gstaiger, Pascal Meier, Ruedi Aebersold
Summary: Protein-protein interactions (PPIs) are the main mode of proteome organization in cells. Traditional PPI networks lack contextual information. Generating context-dependent PPI networks is necessary for structural and systems-level modeling, but remains challenging. In this study, an experimental/computational strategy is described to achieve contextual modeling of PPIs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Agriculture, Dairy & Animal Science
Chenlei Li, Chenglei Song, Kunlong Qi, Yingke Liu, Yaqing Dou, Xiuling Li, Ruimin Qiao, Kejun Wang, Xuelei Han, Xinjian Li
Summary: This study explored a new method for estrus identification by screening salivary proteins related to estrus, providing an important reference for accurate estrus identification of sows, and guiding the development of estrus identification kits/strips.
Article
Pharmacology & Pharmacy
Laura Droctove, Justyna Ciolek, Christiane Mendre, Amelia Chorfa, Paola Huerta, Chrystelle Carvalho, Charlotte Gouin, Manon Lancien, Goran Stanajic-Petrovic, Lorine Braco, Guillaume Blanchet, Gregory Upert, Gregory De Pauw, Peggy Barbe, Mathilde Keck, Gilles Mourier, Bernard Mouillac, Servent Denis, Ricardo C. Rodriguez de la Vega, Loic Quinton, Nicolas Gilles
Summary: This study identified 8 novel mambaquaretin-1 (MQ1) peptides with nanomolar affinities for the V2R, all of which act as antagonists. These MQs form a new subgroup in the Kunitz family, closely related to the non-active dendrotoxins and two V2R-active cobra toxins. Sequence comparison between active and non-active V2R Kunitz peptides revealed key positions involved in V2R interaction. The MQ1-K39A variant showed a higher affinity for the human V2R.
BRITISH JOURNAL OF PHARMACOLOGY
(2022)
Article
Chemistry, Analytical
Rajendra P. Shukla, J. G. Bomer, Daniel Wijnperle, Naveen Kumar, Vihar P. Georgiev, Aruna Chandra Singh, Sivashankar Krishnamoorthy, Cesar Pascual Garcia, Sergii Pud, Wouter Olthuis
Summary: Label-free field-effect transistor-based immunosensors are promising candidates for proteomics and peptidomics-based diagnostics and therapeutics due to their high multiplexing capability, fast response time, and ability to increase the sensor sensitivity due to the short length of peptides. In this study, planar junctionless field-effect transistor sensors were fabricated and characterized for pH sensing. The results show good voltage sensitivity and stability over time, and the experimental verification aligns with theoretical calculations for future applications in detecting peptide-protein interactions.
Article
Chemistry, Applied
Mengru Yu, Shenzhu Lin, Rui Ge, Chunyu Xiong, Linlin Xu, Mengting Zhao, Junfeng Fan
Summary: This study demonstrates a scalable enzymatic approach for generating self-assembly peptides from buckwheat proteins. These peptides exhibit strong self-aggregation capability and form hydrogels with porous texture and remarkable rheological properties. The findings offer opportunities for the use of natural peptide-based hydrogels in various applications.
FOOD HYDROCOLLOIDS
(2022)
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)
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
Chemistry, Applied
Bingxue Jiang, Hongwei Zhang, Jinhua Wang, Yanchao Wang, Xin Du, Yaoguang Chang, Changhu Xue
Summary: In recent years, major yolk proteins (MYPs) have gained more attention. In this study, a method using multiple reactions monitoring mass spectrometry (MRM-MS) was developed to quantify three MYPs. The loss of MYPs during sea cucumber processing was verified by quantitation data of MYPs in sea cucumber body wall and waste liquids. This study not only demonstrated the loss of MYPs during sea cucumber processing, but also highlighted the potential of recycling MYPs from waste water, providing valuable suggestions for maximizing the value of sea cucumbers.
Article
Food Science & Technology
Daqiao Yang, Chunsheng Li, Laihao Li, Yueqi Wang, Yanyan Wu, Shengjun Chen, Yongqiang Zhao, Ya Wei, Di Wang
Summary: Umami peptides formed by microbial metabolism are found to be essential for the umami taste of Chouguiyu. Through peptidomics and metagenomics analysis, this study identified 138 umami peptides and 6 types of proteases from 35 microbial genera during the fermentation process of Chouguiyu. The study also revealed the key microbial strains and proteases involved in the formation of umami peptides. The findings will contribute to improving the umami taste of Chouguiyu through the selection of appropriate proteases and microbial strains.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Multidisciplinary Sciences
Benjamin C. Orsburn, Yuting Yuan, Namandje N. Bumpus
Summary: Single-cell proteomics is a powerful tool for studying cellular heterogeneity and quantifying post-translational modifications. The authors developed a method with improved protein sequence coverage and demonstrated its application in characterizing the effects of inhibitor treatment in single human cells. This approach allows for the detection of multiple classes of post-translational modifications and provides insight into cell-to-cell variability in drug response that is missed by traditional proteomics.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Lana Brockbals, Samara Garrett-Rickman, Shanlin Fu, Maiken Ueland, Dennis McNevin, Matthew P. Padula
Summary: The aim of this study was to investigate the human decomposition process up to 3 months after death and propose novel time-dependent biomarkers for the estimation of decomposition time. An untargeted liquid chromatography tandem mass spectrometry-based bottom-up proteomics workflow was utilized to analyze skeletal muscle, and multiple peptide ratios were successfully proposed as a first step towards generalized, objective biochemical estimation of decomposition time.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Qiao Liu, Qirui Bi, Jingxian Zhang, Weiwei Qin, Shanyong Yi, Qing Hu, Jian Sun, Shen Ji, Ninghua Tan
Summary: This study aims to establish a method based on signature peptides for species authentication of commercial Pheretima. Through DNA barcoding and proteomic analysis, signature peptides of Pheretima were screened and validated, and a simplified sample processing method was developed. The results showed great potential of the method in authenticating commercial Pheretima.
JOURNAL OF PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Carlos H. Vieira-Vieira, Matthias Selbach
Summary: RBPs play a crucial role in posttranscriptional gene expression control, yet their connection with cell signaling is understudied. Methods like RIC and CLIP provide valuable information about RBP-RNA interactions on a genome-wide scale, but biases must be considered to avoid misinterpretation of results.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biology
Patricia Giselle Cipriani, Olivia Bay, John Zinno, Michelle Gutwein, Hin Hark Gan, Vinay K. Mayya, George Chung, Jia-Xuan Chen, Hala Fahs, Yu Guan, Thomas F. Duchaine, Matthias Selbach, Fabio Piano, Kristin C. Gunsalus
Summary: MIP-1 and MIP-2 are novel paralogous C. elegans germ granule components that interact with the MEG-3 protein to promote P granule condensation and localization, playing essential roles in regulating key developmental transitions in the germ line such as stem cell self-renewal, meiotic progression, and gamete differentiation.
Review
Cell Biology
Erik McShane, Matthias Selbach
Summary: Cellular protein degradation is an active and highly regulated process that has diverse roles in biological functions, including homeostasis, regulation, and quality control.
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Immunology
Yikun Yao, Ping Du Jiang, Brittany N. Chao, Deniz Cagdas, Satoshi Kubo, Arasu Balasubramaniyam, Yu Zhang, Bella Shadur, Adeeb NaserEddin, Les R. Folio, Benjamin Schwarz, Eric Bohrnsen, Lixin Zheng, Matthew Lynberg, Simone Gottlieb, Michael A. Leney-Greene, Ann Y. Park, Ilhan Tezcan, Ali Akdogan, Rahsan Gocmen, Sevgen Onder, Avi Rosenberg, Elizabeth J. Soilleux, Errin Johnson, Peter K. Jackson, Janos Demeter, Samuel D. Chauvin, Florian Paul, Matthias Selbach, Haydar Bulut, Menna R. Clatworthy, Zewen K. Tuong, Hanlin Zhang, Benjamin J. Stewart, Catharine M. Bosio, Polina Stepensky, Simon Clare, Sundar Ganesan, John C. Pascall, Oliver Daumke, Geoffrey W. Butcher, Andrew J. McMichael, Anna Katharina Simon, Michael J. Lenardo
Summary: This study describes a new inborn error of immunity caused by mutations in the GTPase of the immune-associated protein 6 (GIMAP6) gene. This condition leads to infections, lymphoproliferation, autoimmunity, and multiorgan vasculitis in affected patients. The study shows that GIMAP6 is involved in autophagy, redox regulation, and polyunsaturated fatty acid (PUFA)-containing lipids. Additionally, GIMAP6 interacts with GABARAPL2 and GIMAP7 to regulate GTPase activity. Furthermore, GIMAP6 is induced by IFN-gamma and plays a critical role in antibacterial immunity. The study also finds that Gimap6(-/-) mice die prematurely due to GIMAP6 deficiency in kidney endothelial cells.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Article
Biochemical Research Methods
Tommaso Mari, Kirstin Moesbauer, Emanuel Wyler, Markus Landthaler, Christian Drosten, Matthias Selbach
Summary: Phosphoproteomics quantifies phosphorylation site changes, but functional analysis is challenging. A new database, iKiP-DB, accurately predicts kinase activity changes and is applied in a SARS-CoV-2 study.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Carlos Henrique Vieira-Vieira, Vita Dauksaite, Anje Sporbert, Michael Gotthardt, Matthias Selbach
Summary: Researchers have developed a quantitative RNA-interactome capture method to assess the function of phosphorylation sites in RNA-binding proteins.
Article
Multidisciplinary Sciences
Ulrike Zinnall, Miha Milek, Igor Minia, Carlos H. Vieira-Vieira, Simon Mueller, Guido Mastrobuoni, Orsalia-Georgia Hazapis, Simone Del Giudice, David Schwefel, Nadine Bley, Franka Voigt, Jeffrey A. Chao, Stefan Kempa, Stefan Huettelmaier, Matthias Selbach, Markus Landthaler
Summary: HDLBP/Vigilin directly interacts with more than 80% of ER-localized mRNAs and plays an important role in the translation of ER-targeted mRNAs. Its absence leads to impaired protein synthesis and secretion, as well as decreased tumor growth.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Medicinal
F. Teresa Melder, Peter Lindemann, Alexander Welle, Vanessa Trouillet, Stefan Heissler, Marc Nazare, Matthias Selbach
Summary: This study presents a novel method for drug interaction screening on cellulose membranes and successfully applies it to the identification of multiple drug targets. The method reliably identifies known targets of natural products in a short period of time, providing an efficient means for drug development.
Article
Biochemistry & Molecular Biology
Tamas Rasko, Amit Pande, Kathrin Radscheit, Annika Zink, Manvendra Singh, Christian Sommer, Gerda Wachtl, Orsolya Kolacsek, Gizem Inak, Attila Szvetnik, Spyros Petrakis, Mario Bunse, Vikas Bansal, Matthias Selbach, Tamas Orban, Alessandro Prigione, Laurence D. Hurst, Zsuzsanna Izsvak
Summary: The study characterizes a new gene PGBD1, specific to nonmonotreme mammals, under purifying selection, retaining original DNA transposon features and capturing additional domains. PGBD1 was found to have important regulatory functions on genes related to neuronal development, with specific binding activity in the core structural RNA NEAT1 of paraspeckles.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Koshi Imami, Matthias Selbach, Yasushi Ishihama
Summary: In this study, we introduced a mass spectrometry-based proteomic method that combines biochemical isolation of mitochondria with pulse stable isotope labeling by amino acids in cell culture, which provides the highest protein identification rate with the shortest measurement time among currently available methods, enabling the quantification of 12 of the 13 mitochondrial-encoded proteins. This method was applied to uncover the global picture of (post-)translational regulation of both mitochondrial- and nuclear-encoded subunits of oxidative phosphorylation complexes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Dermot Harnett, Mateusz C. Ambrozkiewicz, Ulrike Zinnall, Alexandra Rusanova, Ekaterina Borisova, Amelie N. Drescher, Marta Couce-Iglesias, Gabriel Villamil, Rike Dannenberg, Koshi Imami, Agnieszka Munster-Wandowski, Beatrix Fauler, Thorsten Mielke, Matthias Selbach, Markus Landthaler, Christian M. T. Spahn, Victor Tarabykin, Uwe Ohler, Matthew L. Kraushar
Summary: Translation plays a crucial role in modulating the timing and amplification of gene expression during brain development. This study reveals a transient window of dynamic regulation in prenatal brain, where translation upregulation of specific chromatin-binding proteins and downregulation of ribosomal proteins contribute to neuronal subtype differentiation and changes in protein synthesis dynamics. This research highlights the importance of translation in refining transcriptional programs during brain development.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Bo Qin, Simon M. M. Lauer, Annika Balke, Carlos H. H. Vieira-Vieira, Jorg Buerger, Thorsten Mielke, Matthias Selbach, Patrick Scheerer, Christian M. T. Spahn, Rainer Nikolay
Summary: Ribosome biogenesis is a multi-step cellular process that involves the production, processing, folding, and modification of ribosomal RNAs (rRNAs) and ribosomal proteins. By using a minimal in vitro reconstitution system, researchers studied the early assembly phase of the bacterial 50S subunit and found that it occurs in a domain-wise fashion, with late assembly proceeding incrementally. The study also showed that ribosomal proteins and folded rRNA helices induce or stabilize rRNA folds within adjacent regions, creating cooperativity.
NATURE COMMUNICATIONS
(2023)
Meeting Abstract
Biochemical Research Methods
Mirjam Van Bentum, Henrik Zauber, Bertram Klinger, Mohamed Haji, Philipp Mertins, Nils Bluethgen, Matthias Selbach
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Oncology
Hamed Alborzinia, Andres F. Florez, Sina Kreth, Lena M. Brueckner, Umut Yildiz, Moritz Gartlgruber, Dorett Odoni, Gernot Poschet, Karolina Garbowicz, Chunxuan Shao, Corinna Klein, Jasmin Meier, Petra Zeisberger, Michal Nadler-Holly, Matthias Ziehm, Franziska Paul, Juergen Burhenne, Emma Bell, Marjan Shaikhkarami, Roberto Wuerth, Sabine A. Stainczyk, Elisa M. Wecht, Jochen Kreth, Michael Buettner, Naveed Ishaque, Matthias Schlesner, Barbara Nicke, Carlo Stresemann, Maria Llamazares-Prada, Jan H. Reiling, Matthias Fischer, Ido Amit, Matthias Selbach, Carl Herrmann, Stefan Woelfl, Kai-Oliver Henrich, Thomas Hoefer, Andreas Trumpp, Frank Westermann
Summary: The study reveals that MYCN-amplified neuroblastoma undergoes ferroptosis in the absence of cysteine, suggesting a potential therapeutic approach of combining cysteine depletion and GPX4 inactivation. In addition, the study provides evidence that targeting multiple ferroptosis targets can be a promising therapeutic strategy for aggressive MYCN-amplified tumors.
Article
Biochemistry & Molecular Biology
Ethiraj Ravindran, Ramona Juehlen, Carlos H. Vieira-Vieira, Thuong Ha, Yuval Salzberg, Boris Fichtman, Lena Luise-Becker, Nuno Martins, Sylvie Picker-Minh, Paraskevi Bessa, Peer Arts, Matilda R. Jackson, Ajay Taranath, Benjamin Kamien, Christopher Barnett, Na Li, Victor Tarabykin, Gisela Stoltenburg-Didinger, Amnon Harel, Matthias Selbach, Achim Dickmanns, Birthe Fahrenkrog, Hao Hu, Hamish Scott, Angela M. Kaindl
Summary: Biallelic variants in the NUP85 gene have been found to cause MCPH-SCKS spectrum disorders, expanding the phenotypic spectrum of NUP85-related diseases and suggesting a role for NUP85 in nervous system development.
HUMAN MOLECULAR GENETICS
(2021)
