Article
Multidisciplinary Sciences
Kevin L. Yang, Fengchao Yu, Guo Ci Teo, Kai Li, Vadim Demichev, Markus Ralser, Alexey I. Nesvizhskii
Summary: This article presents an accessible method to improve peptide spectrum match rescoring using deep learning predictions in bottom-up proteomics. The authors demonstrate significant improvements in peptide/protein identifications across various experiments, including single-cell proteomics and immunopeptidomics. They introduce a new tool called MSBooster, which incorporates deep learning-based predictions of peptide properties to rescore peptide-to-spectrum matches, and show its utility in different workflows, such as immunopeptidomics and single-cell proteomics.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Neil A. McCracken, Sarah A. Peck Justice, Aruna B. Wijeratne, Amber L. Mosley
Summary: The study introduces a user-friendly analysis of the melt shift calculation workflow and quantitatively assesses the impact of key steps in the analysis workflow on the final output list of stabilized and destabilized proteins. It also presents a more optimized analysis workflow, illustrating the importance of selected calculation steps on the final list of reported proteins of interest in a study. The development of the R based program Inflect offers a valuable resource for the research community to analyze data from TPP and CETSA experiments.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Maria Joao Sebastiao, Michael Hoffman, Jose Escandell, Fatemeh Tousi, Jin Zhang, Bruno Figueroa, Christine DeMaria, Patricia Gomes-Alves
Summary: Monoclonal antibody-based therapy has proven effective against various diseases, but the co-production of mispaired species can reduce its efficacy and increase production costs. This study used transcriptomics and proteomics analyses to identify signaling pathways associated with low and high mispairing clone signatures. The results showed that high mispairing clones exhibited activated endoplasmic reticulum stress, while low mispairing clones had profiles indicative of activated protein translation. Additionally, a group of genes was identified as potential biomarkers for early detection of high mispairing levels.
Article
Biochemical Research Methods
Jinjun Gao, Yuan Liu, Fan Yang, Xuemin Chen, Benjamin F. Cravatt, Chu Wang
Summary: ABPP is a powerful chemical proteomic method for studying protein activity, modifications, and interactions, where accurate quantification is crucial. CIMAGE is a specialized quantification software for ABPP data analysis, providing efficient and accurate quantification with the ability to visualize results conveniently.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Runmin Yang, Jingjing Ma, Shu Zhang, Yu Zheng, Lusheng Wang, Daming Zhu
Summary: This study introduces a new storage format called mzMD for MS datasets and presents an algorithm to query this format for summarizing a given data window. Experimental results demonstrate the high speed and stability of mzMD in retrieving high-quality data window summaries.
Article
Biochemical Research Methods
Xuantang Wang, Guoquan Yan, Haoyang Zheng, Mingxia Gao, Xiangmin Zhang
Summary: This study demonstrated a strategy combining array-based online two-dimensional liquid chromatography and liquid chromatography-tandem mass spectrometry for high throughput and in-depth identification of protein complexes from cultured human HeLa cell extracts. By utilizing an array parallel strategy, the analysis throughput was significantly increased, enabling the discovery of numerous protein complexes and the construction of a PPI network among them.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Biochemical Research Methods
Kyle J. Juetten, Jennifer S. Brodbelt
Summary: MS-TAFI is a free Python-based program for analyzing and visualizing deconvoluted MS/MS data of intact proteins, offering a streamlined approach to data analysis. It also includes tools for native mass spectrometry experiments, allowing for the search of fragment ions with retained ligands and visualization of charge site locations.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Diana Canetti, Francesca Brambilla, Nigel B. Rendell, Paola Nocerino, Janet A. Gilbertson, Dario Di Silvestre, Andrea Bergamaschi, Francesca Lavatelli, Giampaolo Merlini, Julian D. Gillmore, Vittorio Bellotti, Pierluigi Mauri, Graham W. Taylor
Summary: Amyloidosis is a rare human disease caused by abnormal protein deposition in tissues, with proteomic analysis playing a crucial role in clinical diagnosis and amyloid typing. Inter-center data exchange is effective for testing and validating the accuracy of different software platforms in proteomics analysis.
Article
Chemistry, Applied
Lingrong Wen, Yueming Jiang, Xuesong Zhou, Huimin Bi, Bao Yang
Summary: Soybean peptides are functional foods with health benefits, with their structure playing a key role in determining these benefits. By identifying peptide structure and evaluating immunomodulatory activity, soybean peptides were found to facilitate macrophage proliferation.
Article
Biochemical Research Methods
Soroosh Gholamizoj, Bin Ma
Summary: SPEQ is a spectrum quality assessment tool that classifies spectra into high-quality and low-quality using a deep neural network, which has demonstrated improved prediction accuracy compared to other models.
Article
Biochemical Research Methods
Chenxin Li, Mingxuan Gao, Wenxian Yang, Chuanqi Zhong, Rongshan Yu
Summary: Diamond is a multi-modal DIA-MS data processing pipeline based on Nextflow and containerization, integrating SCS and PCS strategies for cases with and without assay libraries. This versatile toolbox enables large-scale peptide identification and quantification in DIA data, while being user-friendly and easily extendable.
Review
Biotechnology & Applied Microbiology
Juergen Cox
Summary: Proteomics is undergoing a transformation with the use of deep learning methods to predict peptide fragmentation spectra. These methods have superseded traditional approaches and shown improved sensitivity and specificity in peptide identification. Machine learning has significant applications in immunopeptidomics and proteogenomics, although challenges remain in predicting spectra for modified peptides and cross-linked peptide pairs.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Mohd Afiq Hazlami Habib, Mohd Nazri Ismail
Summary: The fruit and leaf of God's crown plant have been traditionally used for treating various diseases. However, the proteins of this tropical plant are still not well studied. Three protein extraction methods were compared for their efficiency in recovering proteins from the plant, with the phenol extraction method showing the highest percentage of protein recovery. Liquid chromatography-tandem mass spectrometry analysis revealed that proteins identified through the phenol extraction method included a significant percentage of enzymatic proteins with various biological functions.
JOURNAL OF FOOD BIOCHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Sebastian Didusch, Moritz Madern, Markus Hartl, Manuela Baccarini
Summary: amica is a web-based software that can handle proteomic data and provide quality control, differential expression, biological network, and over-representation analysis. Users can compare multiple conditions and quickly identify enriched or depleted proteins through the interactive query interface. The results can be visualized using customized output graphics and exported in a tab-separated format for sharing.
Article
Biotechnology & Applied Microbiology
Christoph Keysberg, Oliver Hertel, Louise Schelletter, Tobias Busche, Chiara Sochart, Jorn Kalinowski, Raimund Hoffrogge, Kerstin Otte, Thomas Noll
Summary: CHO cells derived from Chinese hamster ovaries are widely used in biopharmaceutical production, but research on exosomes in these cells is scarce. Exosomes are considered a universal mediator of intercellular communication and a proposed new drug delivery format in biopharmaceuticals. This study analyzed the proteome and RNA of exosomes from CHO-K1 cells, providing reference data for future research.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Nga Lao, Niall Barron
Summary: m6A modification on eukaryotic mRNA plays a crucial role in cellular processes. This study demonstrates that manipulating the expression of m6A readers, YTHDF1, 2, and 3, can enhance recombinant protein yield and viral protein expression in mammalian cells. These findings suggest the potential of utilizing epitranscriptomic-based approaches for improving protein production and viral vector yield in host cell line engineering.
BIOTECHNOLOGY JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Giulia Borsi, Krishna Motheramgari, Heena Dhiman, Martina Baumann, Elly Sinkala, Max Sauerland, Julian Riba, Nicole Borth
Summary: This study investigated the variability and diversity of individual cell transcriptomes in CHO and HEK293 cells under different culture conditions using full-length coverage single-cell RNA sequencing. The results showed a batch effect in CHO cells and highlighted the impact of the cell cycle on transcriptome variation.
JOURNAL OF BIOTECHNOLOGY
(2023)
Article
Endocrinology & Metabolism
Zora Messner, David Carro-Vazquez, Judith Haschka, Johannes Grillari, Heinrich Resch, Christian Muschitz, Peter Pietschmann, Jochen Zwerina, Matthias Hackl, Roland Kocijan
Summary: This study investigated circulating miRNAs as potential biomarkers for monitoring treatment response in women with postmenopausal osteoporosis on denosumab therapy. The results showed significant changes in expression of seven miRNAs after two years of treatment, which correlated with changes in bone mineral density and bone turnover markers.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2023)
Article
Ecology
Birgit Gemeinholzer, Oliver Rupp, Annette Becker, Marc Strickert, Christina M. Mueller
Summary: Red clover is an important forage crop grown worldwide for cattle feed and soil improvement. There is a lack of knowledge about the natural genetic and phenotypic diversity of red clover. This study developed a low-cost mRNA analysis method and compared it with population genetic data to assess intraspecific variation and transcriptome responses.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Nikolaus Virgolini, Marco Silvano, Ryan Hagan, Ricardo Correia, Paula M. Alves, Colin Clarke, Antonio Roldao, Ines A. Isidro
Summary: Using single-cell RNA sequencing, this study performed transcriptomics analysis of Sf9 insect cells during the production of rAAV2. The study found an increase in transcriptional heterogeneity during infection, which was linked to the expression of baculovirus genes and rAAV2 transgenes. Additionally, the study highlighted limitations of the dual-baculovirus system in producing rAAV2 particles.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Oleh Lushchak, Markus Schosserer, Johannes Grillari
Summary: Cellular senescence refers to a stable cell cycle arrest state with specific characteristics. Senescent cells accumulate in the body during normal aging, limiting lifespan and promoting aging-related as well as unrelated diseases. Diseases associated with cellular senescence are referred to as senopathies, and targeting senescent cells through senolytics or senomorphics may help mitigate these diseases. Animal studies provide mechanistic evidence for the connection between senescent cell accumulation and disease progression in various senopathies, including cardiovascular, metabolic, musculoskeletal, liver, kidney, lung diseases, and neurodegeneration. The development of novel senotherapies is hindered by the heterogeneity of senescence phenotypes, resulting in a lack of universal biomarkers and difficulties in distinguishing senescent from non-senescent cells.
Article
Genetics & Heredity
Johanna Nelkner, Liren Huang, Timo W. W. Lin, Alexander Schulz, Benedikt Osterholz, Christian Henke, Jochen Blom, Alfred Puehler, Alexander Sczyrba, Andreas Schlueter
Summary: The family Nitrososphaeraceae is important in agricultural microbiomes. Metabolic reconstruction of Thaumarchaeota MAGs from German soil showed their relevance for soil fertility and plant health. This family plays a crucial role in agricultural soil microbial communities.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Gastroenterology & Hepatology
Patrick Starlinger, Laura Brunnthaler, Chantal McCabe, David Pereyra, Jonas Santol, Jessica Steadman, Matthias Hackl, Susanna Skalicky, Hubert Hackl, Raphael Gronauer, Daniel O'Brien, Renate Kain, Petra Hirsova, Gregory J. Gores, Chen Wang, Thomas Gruenberger, Rory L. Smoot, Alice Assinger
Summary: Through the analysis of blood and tissue samples from patients, this study explores the early transcriptional changes during liver regeneration and their differences in individuals with dysfunctional liver regeneration.
Article
Multidisciplinary Sciences
Dewi Pramanik, Annette Becker, Clemens Roessner, Oliver Rupp, Diego Bogarin, Oscar Alejandro Perez-Escobar, Anita Dirks-Mulder, Kevin Droppert, Alexander Kocyan, Erik Smets, Barbara Gravendeel
Summary: This study analyzes the evolution and development of fruit dehiscence zones in orchids. Gene expression analysis reveals that orchids have different fruit dehiscence mechanisms compared to Arabidopsis thaliana. Genes involved in carpel, gynoecium, ovule development, and lipid biosynthesis may play a novel role in the formation of dehiscence zone tissues in orchids.
Article
Multidisciplinary Sciences
Diana Swolin-Eide, Gun Forsander, Auste Pundziute Lycka, Daniel Novak, Johannes Grillari, Andreas B. Diendorfer, Matthias Hackl, Per Magnusson
Summary: This case-control study aimed to investigate potential differences in circulating miRNAs between young individuals with long-duration type 1 diabetes (T1D) and healthy controls, as well as the expression of these identified miRNAs across different tissues. The results showed that 27 miRNAs were upregulated and one was downregulated in T1D. Six of these miRNAs were tissue-enriched. These findings have important implications for studying biomarkers for diabetes-related complications.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Lucie Schroeder, Oliver Rupp, Michael Senkler, Nils Rugen, Natalija Hohnjec, Alexander Goesmann, Helge Kuester, Hans-Peter Braun
Summary: European mistletoe is a hemiparasitic flowering plant with an extremely large genome size. A transcriptome project was conducted to study its gene space, resulting in a database containing sequences of thousands of open reading frames encoding distinct proteins. A new database, VaGs II, was developed by combining data from a summer and winter transcriptome project, and it showed a higher completeness compared to the previous database. The quality of the new database was evaluated by re-analyzing proteome data, which provided new insights into the oxidative phosphorylation system of European mistletoe.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Julia Hassa, Tom Jonas Tubbesing, Irena Maus, Robert Heyer, Dirk Benndorf, Mathias Effenberger, Christian Henke, Benedikt Osterholz, Michael Beckstette, Alfred Puehler, Alexander Sczyrba, Andreas Schlueter
Summary: This study used metagenomic and metaproteomic analyses to investigate the microbial communities in a full-scale biogas plant with three differently operated digesters. The results showed that these microbial communities had a significant impact on the abundance of enzymes and genes involved in the biogas process, and identified key microorganisms involved in different steps of anaerobic digestion. Further analysis of the highly abundant MAGs in all digesters indicated their potential in ensuring biogas process stability.
Article
Physiology
Matthijs Luxen, Peter J. Zwiers, Femke Meester, Rianne M. Jongman, Timara Kuiper, Jill Moser, Marianne Pultar, Susanna Skalicky, Andreas B. Diendorfer, Matthias Hackl, Matijs van Meurs, Grietje Molema
Summary: This study investigated the microRNA and mRNA transcription patterns in different microvascular compartments of the mouse kidney cortex. Unique microRNA and mRNA profiles were identified, providing important molecular information for studying microvascular heterogeneity in the kidney in health and disease.
AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY
(2023)
Review
Materials Science, Multidisciplinary
Elisaveta Snezhkova, Heinz Redl, Johannes Grillari, Marcin Osuchowski
Summary: This article introduces the application of activated carbon or charcoal in alleviating inflammation and explains its mechanisms of protecting the microbiome and bone marrow, as well as its anti-inflammatory and anti-oxidant effects. Early application of activated carbon and its high adsorption capacity are essential in the treatment of preventing sepsis and multi-organ failure.
C-JOURNAL OF CARBON RESEARCH
(2023)
