Article
Biochemical Research Methods
Julien Slagboom, Rico J. E. Derks, Raya Sadighi, Govert W. Somsen, Chris Ulens, Nicholas R. Casewell, Jeroen Kool
Summary: In this study, the authors developed a new analytical strategy called high-throughput (HT) venomics, capable of performing a full proteomic analysis of snake venom in a short time. The strategy involves RP-HPLC-nanofractionation analytics, mass spectrometry analysis, in-solution tryptic digestion, and high-throughput proteomics. The authors also developed scripts to process and analyze the obtained data. They applied this strategy to venom samples from various medically important snake species and found it to be a valuable tool for studying venom variation.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Juho Heininen, Ulrika Julku, Timo Myohanen, Tapio Kotiaho, Risto Kostiainen
Summary: A new multiplexed LC-MS/MS method was developed for analyzing amino acids in mouse brain microdialysis samples, providing good chromatographic performance and high sensitivity. The method showed good repeatability and linearity, indicating its quantitative performance. The method was sensitive enough to detect low concentrations of amino acids in brain microdialysis samples.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Biochemical Research Methods
Ilya I. Pikovskoi, Dmitry S. Kosyakov
Summary: In this study, Kendrick mass defect (KMD) analysis was used to identify oligomer series with different polymerization degrees and structurally related compounds in the Orbitrap mass spectra of Siberian pine dioxane lignin preparation. It was shown that KMD analysis can effectively determine the elemental compositions and structures of oligomers with high molecular weights (> 1 kDa), and was also applied to interpret complex tandem mass spectra and establish main collision-induced dissociation pathways.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Review
Pharmacology & Pharmacy
Qi Xiao, Fangfei Zhang, Luang Xu, Liang Yue, Oi Lian Kon, Yi Zhu, Tiannan Guo
Summary: This paper summarizes the advances and limitations of biomarkers in cancer research, as well as the important applications of mass spectrometry technology in proteomics. The article emphasizes the role of artificial intelligence technology in clinical studies, as well as the importance of combining computational and statistical methods in biomarker research.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Article
Medical Laboratory Technology
Angela Mc Ardle, Aleksandra Binek, Annie Moradian, Blandine Chazarin Orgel, Alejandro Rivas, Kirstin E. Washington, Conor Phebus, Danica-Mae Manalo, James Go, Vidya Venkatraman, Casey W. Coutelin Johnson, Qin Fu, Susan Cheng, Koen Raedschelders, Justyna Fert-Bober, Stephen R. Pennington, Christopher Murray, Jennifer E. Van Eyk
Summary: This study developed standardized workflows for detecting circulating protein biomarkers in different blood matrices, achieving reproducible and quantifiable analysis by optimizing sample preparation and mass spectrometry. The workflows allowed for sensitive high-throughput or deeper profiling analysis, with reliable results across different biofluids. By describing the observable, reliable, reproducible, and quantifiable proteomes for each biofluid and workflow, the researchers aim to simplify discovery approaches and facilitate the translation of candidate markers into clinical use.
CLINICAL CHEMISTRY
(2022)
Review
Biochemical Research Methods
Shuting Xu, Cheng Yang, Xiuping Yan, Huwei Liu
Summary: Mass spectrometry is utilized for single-cell analysis due to its sensitivity and dynamic ranges, with recent advancements focusing on improving automation and throughput to address challenges in manual techniques. Strategies have been developed to enhance information coverage and achieve comprehensive single-cell multiomics data during high throughput detection, providing a promising outlook for single-cell research.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Engineering, Environmental
Yibei Wan, Chong Xing, Xinyu Wang, Zhaomin Yang, Xiangpeng Huang, Xinlei Ge, Lin Du, Qiongqiong Wang, Huan Yu
Summary: We present a data analysis workflow for nontarget tandem high-resolution mass spectrometry (MS) that allows for the comprehensive classification of functionalized organic compounds in complex atmospheric samples. With a single mass spectrometry run, the workflow provides molecular formula, functional group, and aromaticity information for a large percentage of deprotonated and protonated molecules. The assignment and quantification of functional groups can be used to trace the sources, formation, and aging of organic compounds in the atmosphere.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2022)
Article
Chemistry, Analytical
Robert S. Plumb, Thomas McDonald, Paul D. Rainville, Jason Hill, Lee A. Gethings, Kelly A. Johnson, Ian D. Wilson
Summary: Vacuum jacketed column (VJC) technology can significantly improve the performance of UHPLC systems, enhancing chromatographic separation and increasing detection capabilities for metabolites. Using the VJC system can reduce peak tailing, increase peak capacity, and enhance the intensity and response of MS peaks.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Zhiwei Tu, Henk L. Dekker, Winfried Roseboom, Bhagyashree N. Swarge, Peter Setlow, Stanley Brul, Gertjan Kramer
Summary: The research investigated the proteome dynamics during sporulation of Bacillus subtilis vegetative cells under nutrient limitation. Protein co-expression analysis identified four modules, with brown and green modules being upregulated during sporulation containing proteins associated with sporulation, while blue module showed negative correlation and contained ribosomal and metabolic proteins. Besides known transcription regulons, some proteins co-expressed with brown and green modules may also play roles during sporulation. Levels of some coat proteins decreased late in sporulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Jason Derks, Nikolai Slavov
Summary: Accurate protein quantification is crucial for identifying protein markers, regulatory relationships, and pathophysiological mechanisms. The plexDIA framework allows for parallel analysis of precursors and samples, increasing proteomics throughput. Improvements in retention time estimates within plexDIA lead to more precise protein quantification. Future directions for plexDIA include optimizing mass-tags, introducing isotopologous carriers, and developing algorithms for enhanced sensitivity and proteome coverage. These advancements will enable high-throughput functional proteomic assays, including single-cell analysis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Dorothea Mylopotamitaki, Florian S. Harking, Alberto J. Taurozzi, Zandra Fagernas, Ricardo M. Godinho, Geoff M. Smith, Marcel Weiss, Tim Schueler, Shannon P. McPherron, Harald Meller, Joo Cascalheira, Nuno Bicho, Jesper V. Olsen, Jean-Jacques Hublin, Frido Welker
Summary: High-throughput proteomic analysis of archaeological skeletal remains can provide valuable information about past fauna community compositions and species dispersals. However, the extraction of ancient proteins from bone specimens is challenging due to degradation. In this study, six proteomic extraction methods were compared on Late Pleistocene remains with different levels of proteome preservation. The results showed that simple acid-insoluble extraction methods performed better in highly degraded contexts, while for well-preserved specimens, the approach using EDTA demineralization and protease-mix proteolysis yielded the highest number of identified peptides.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Thomas J. M. Michiels, Madelief A. van Veen, Hugo D. Meiring, Wim Jiskoot, Gideon F. A. Kersten, Bernard Metz
Summary: Animal tests are currently used to confirm the efficacy and safety of toxoid vaccines, but in vitro assays may replace them if production consistency can be proven. A TMT labeling method based on a common reference allows for faster analysis time and the identification of suitable candidate peptides for quality control assays.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Analytical
Qian Kong, Yicheng Weng, Zhendong Zheng, Wendong Chen, Pengfei Li, Zongwei Cai, Ruijun Tian
Summary: Tyrosine phosphorylation plays a crucial role in signaling pathways, but its systematic analysis is challenging due to its low abundance and transient nature. In this study, a 96-well microplate-based approach was developed to simplify the pTyr peptide enrichment workflow and showed high sensitivity and reproducibility.
ANALYTICAL CHEMISTRY
(2022)
Review
Cell Biology
Md Zahirul Islam Khan, Shing Yau Tam, Helen Ka Wai Law
Summary: Gastrointestinal cancers (GICs) are the most diagnosed cancers and the leading cause of cancer-related death globally. Deficiency of effective early diagnostic biomarkers contributes to poor prognosis and treatment outcomes. Proteomics study and its functional analysis hold promise in improving early diagnosis and management of GICs. Challenges remain in validating proteomics-based biomarkers for translation into clinical practice.
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
Biochemical Research Methods
Annika Cimdins-Ahne, Alexey Chernobrovkin, Soo-Kyoung Kim, Vincent T. Lee, Roman A. Zubarev, Ute Romling
Summary: Ligand binding to macromolecules can change their characteristics, and cyclic di-GMP is a second messenger involved in bacterial lifestyle transition. However, the number of cyclic di-GMP receptors is limited. To facilitate screening for cyclic di-nucleotide binding proteins, a non-radioactive method using MALDI-TOF was developed. The results showed that a specific variant can bind cyclic di-GMP.
JOURNAL OF MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Margit Kaldmae, Thibault Vosselman, Xueying Zhong, Dilraj Lama, Gefei Chen, Mihkel Saluri, Nina Kronqvist, Jia Wei Siau, Aik Seng Ng, Farid J. Ghadessy, Pierre Sabatier, Borivoj Vojtesek, Medoune Sarr, Cagla Sahin, Nicklas Osterlund, Leopold L. Ilag, Venla A. Vaananen, Saikiran Sedimbi, Marie Arsenian-Henriksson, Roman A. Zubarev, Lennart Nilsson, Philip J. B. Koeck, Anna Rising, Axel Abelein, Nicolas Fritz, Jan Johansson, David P. Lane, Michael Landreh
Summary: Disordered proteins pose challenges to structural biology. Researchers have found that fusing the protein with a highly soluble spider silk domain can modulate its characteristics and enhance translation efficiency. This mechanism is of great significance for cancer treatment.
Article
Chemistry, Physical
Boyang Guo, Sudarsana Reddy Vanga, Ximena Lopez-Lorenzo, Patricia Saenz-Mendez, Sara Ronnblad Ericsson, Yuan Fang, Xinchen Ye, Karen Schriever, Eva Backstrom, Antonino Biundo, Roman A. Zubarev, Istvan Furo, Minna Hakkarainen, Per-Olof Syren
Summary: In the biodegradation of plastics, the conformational selection of enzymes and substrates plays a crucial role. Studies utilizing molecular dynamics simulations and experimental validation have shown that enzyme engineering can alter enzyme conformation, affecting its binding capability with substrates. Matching enzyme and substrate conformations can enhance the efficiency of plastic hydrolysis.
Article
Clinical Neurology
Jijing Wang, Cong Guo, Zhaowei Meng, Marissa D. Zwan, Xin Chen, Sven Seelow, Susanna L. Lundstrom, Sergey Rodin, Charlotte E. Teunissen, Roman A. Zubarev
Summary: This study strengthens the association between isoAsp and Alzheimer's disease (AD) using novel approaches to isoAsp analysis in blood samples. The findings demonstrate elevated isoAsp levels, reduced anti-isoAsp antibodies, increased A beta concentration, and more protein aggregation in AD blood compared to controls. Additionally, deamidation reduces the binding capacity of blood protein HSA with A beta and p-tau.
ALZHEIMERS & DEMENTIA
(2023)
Article
Biochemical Research Methods
Zeljka Popovic, Lissa C. Anderson, Xuepei Zhang, David S. Butcher, Greg T. Blakney, Roman A. Zubarev, Alan G. Marshall
Summary: Isotopic depletion of growth medium improves protein mass measurement accuracy and signal-to-noise ratio, enabling better mass spectrometry analysis for both bacteria and eukaryotes.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Immunology
Abdul Muktadir Shafi, Akos Vegvari, Roman A. Zubarev, Carlos Penha-Goncalves
Summary: This study reveals the important role of the STING-INFb-CXCL10 pathway in brain microvascular endothelial cells (BECs) in the development of cerebral malaria (CM). Activation of this pathway leads to immunoproteasome activation, enhanced antigen presentation, and impairment of endothelial barrier function. These findings provide insights into the pathogenesis of CM and its lethality.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Medicine, Research & Experimental
Huqiao Luo, Vilma Urbonaviciute, Amir Ata Saei, Hezheng Lyu, Massimiliano Gaetani, Akos Vegvari, Yanpeng Li, Roman A. Zubarev, Rikard Holmdahl
Summary: Mutations in NCF1 gene that cause low production of ROS are strongly linked to systemic lupus erythematosus. The deficiency of ROS in plasmacytoid dendritic cells (pDCs) exacerbates lupus development by promoting pDC accumulation in multiple organs, elevating IFN-alpha levels, and activating IFN-stimulated genes. Mechanistic studies show that ROS deficiency enhances pDC generation and migration, which further augment type I IFN responses. Restoring NOX2-derived ROS specifically in pDCs protects against lupus by suppressing these pathways.
Article
Hematology
Anna Rydstrom, Tan H. M. Grahn, Abhishek Niroula, Els Mansell, Mark van der Garde, Maroulio Pertesi, Agatheeswaran Subramaniam, Shamit Soneji, Roman Zubarev, Tariq Enver, Bjorn Nilsson, Kenichi Miharada, Jonas Larsson, Stefan Karlssona
Summary: This study provides a detailed functional and molecular characterization of HSCs at different phases of regeneration and identifies a gene set associated with the transition from proliferation to quiescence.
EXPERIMENTAL HEMATOLOGY
(2023)
Article
Immunology
Mike Aoun, Ana Coelho, Alexander Kramer, Amit Saxena, Pierre Sabatier, Christian Michel Beusch, Erik Lonnblom, Manman Geng, Nhu-Nguyen Do, Zhongwei Xu, Jingdian Zhang, Yibo He, Laura Romero Castillo, Hassan Abolhassani, Bingze Xu, Johan Viljanen, Joanna Rorbach, Gonzalo Fernandez Lahore, Inger Gjertsson, Alf Kastbom, Christopher Sjowall, Jan Kihlberg, Roman A. Zubarev, Harald Burkhardt, Rikard Holmdahl
Summary: The study reveals that autoreactive antigen-specific naive B cells tolerize infiltrating T cells against self-antigens to impede the development of tissue-specific autoimmune inflammation.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Biochemical Research Methods
Akos Vegvari, Xuepei Zhang, Roman A. Zubarev
Summary: This study successfully detected proteins from individual Escherichia coli bacteria for the first time, with validation of the findings through comparison with other samples and bulk proteomics data.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Irina D. D. Vasileva, Tatiana Yu. Samgina, Zhaowei Meng, Roman A. A. Zubarev, Albert T. T. Lebedev
Summary: In traditional proteomic analysis, disulfide bonds in peptides pose a problem for sequencing, requiring multiple reaction steps. However, this study found that EThcD technology can sequence peptides with disulfide bonds without the need for chemical derivatization.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Tatiana Yu. Samgina, Irina D. Vasileva, Polonca Trebse, Gregor Torkar, Alexey K. Surin, Zhaowei Meng, Roman A. Zubarev, Albert T. Lebedev
Summary: Peptides released on frogs' skin in a stress situation are their only weapon against micro-organisms and predators. Each frog population has its own unique peptidome suitable for their habitat. This study analyzed the peptidome composition of the Central Slovenian agile frog population, and discovered multiple peptide families.
Article
Biochemistry & Molecular Biology
Amir Ata Saei, Hassan Gharibi, Hezheng Lyu, Brady Nilsson, Maryam Jafari, Hans Von Holst, Roman A. Zubarev
Summary: The study investigated the molecular consequences of traumatic brain injuries using a proteomics approach. It found that dynamic impacts led to reduced neuron viability and significant changes in protein solubility. The affected proteins were involved in various pathways, including cell adhesion, stress response, immune response, complement, and coagulation cascades.
Article
Multidisciplinary Sciences
Shane C. Wright, Aikaterini Motso, Stefania Koutsilieri, Christian M. Beusch, Pierre Sabatier, Alessandro Berghella, Elodie Blondel-Tepaz, Kimberley Mangenot, Ioannis Pittarokoilis, Despoina-Christina Sismanoglou, Christian Le Gouill, Jesper V. Olsen, Roman A. Zubarev, Nevin A. Lambert, Alexander S. Hauser, Michel Bouvier, Volker M. Lauschke
Summary: This study investigates the subcellular location of GLP-1R signaling events and reveals associations between signaling profiles and adverse drug reactions, providing important insights for rational drug design and improving the therapeutic potential of GLP-1R agonists.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Zhongwei Xu, Bingze Xu, Susanna L. Lundstrom, Alex Moreno-Giro, Danxia Zhao, Myriam Martin, Erik Lonnblom, Qixing Li, Alexander Kramer, Changrong Ge, Lei Cheng, Bibo Liang, Dongmei Tong, Roma Stawikowska, Anna M. Blom, Gregg B. Fields, Roman A. Zubarev, Rikard Holmdahl
Summary: This study developed antibodies targeting type-II collagen and investigated their mechanism of action. The antibody R69-4 inhibits autoantibody-mediated arthritis by hindering FCGR3 signaling, highlighting its potential clinical utility in acute rheumatoid arthritis.
NATURE COMMUNICATIONS
(2023)