Article
Gastroenterology & Hepatology
Christoph Stingl, Angela Bureo Gonzalez, Coskun Guzel, Kai Yi Nadine Phoa, Michail Doukas, Gerben Eise Breimer, Sybren Lodewijk Meijer, Jacques Johannes Bergman, Theo Marten Luider
Summary: The study investigated significant proteomic changes during the progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC), revealing an overall up-regulation in protein abundance and diversity in dysplastic/EAC tissue compared to non-dysplastic BE. Validation of higher expression of MSH6 and XPO5 confirmed the findings, with further analysis indicating alterations in pathways related to carcinogenesis such as micro-RNA trafficking, DNA damage repair, and spliceosome activity in dysplastic/EAC tissue.
JOURNAL OF GASTROENTEROLOGY
(2021)
Article
Chemistry, Multidisciplinary
Jorunn Stamnaes, Daniel Stray, Maria Stensland, Vikas K. Sarna, Tuula A. Nyman, Knut E. A. Lundin, Ludvig M. Sollid
Summary: In patients with celiac disease (CeD) who have been effectively treated with a gluten-free diet, different degrees of tissue inflammation response are observed after gluten challenge, indicating the presence of low-grade tissue inflammation and antigluten immunity. Histological assessment alone may not be sufficient to evaluate the full recovery and gut mucosal healing of CeD patients. There is a concern that a seemingly proper gluten-free diet may not be able to completely control gut inflammation in all CeD patients.
Article
Biochemical Research Methods
Firat Kaya, Matthew D. Zimmerman, Rosleine Antilus-Sainte, Martin Gengenbacher, Claire L. Carter, Veronique Dartois
Summary: This study developed a workflow that combines laser-capture microdissection and mass spectrometry imaging to investigate the spatial distribution and quantitation of small molecule drugs in bones. The optimized staining methods enabled simultaneous histology staining and mass spectrometry imaging, revealing drug accumulation in bone tissue architecture.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Clinical Neurology
Dominique F. Leitner, Christopher William, Arline Faustin, Manor Askenazi, Evgeny Kanshin, Matija Snuderl, Declan McGuone, Thomas Wisniewski, Beatrix Ueberheide, Laura Gould, Orrin Devinsky
Summary: This study used mass spectrometry to analyze the differential protein expression in frontal cortex and hippocampus of sudden unexplained death in childhood (SUDC) cases. The results showed activated oxidative phosphorylation and inhibited EIF2 signaling in the frontal cortex, and activated acute phase response in the hippocampus, suggesting potential mechanisms for SUDC. The weighted gene correlation network analysis of clinical history also revealed modules associated with viral pathology, fever, and febrile seizure history.
ACTA NEUROPATHOLOGICA
(2022)
Article
Biochemical Research Methods
Danting Liu, Shu Yang, Kanisha Kavdia, Jeffrey M. Sifford, Zhiping Wu, Boer Xie, Zhen Wang, Vishwajeeth R. Pagala, Hong Wang, Kaiwen Yu, Kaushik Kumar Dey, Anthony A. High, Geidy E. Serrano, Thomas G. Beach, Junmin Peng
Summary: A streamlined protocol has been developed to quantify over 9000 proteins with 0.5 μg of protein using 16-plex TMT coupled with LC/LC-MS/MS. Comparison with the standard protocol in 16 human brain tissue samples showed that the microgram-scale protocol had adequate sensitivity and reproducibility to detect differentially expressed proteins in disease-related pathways. This newly developed method holds promise for deep proteomic analysis at sub-microgram levels in biological and clinical samples.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Nicolai Bjodstrup Palstrom, Aleksandra M. Rojek, Hanne E. H. Moller, Charlotte Toftmann Hansen, Rune Matthiesen, Lars Melholt Rasmussen, Niels Abildgaard, Hans Christian Beck
Summary: Amyloidosis is a rare disease caused by the misfolding and aggregation of proteins, and accurate identification of the specific proteins is crucial for treatment choice. Mass spectrometry-based proteomics has become the preferred method for identifying the amyloidogenic protein. However, manual interpretation of the data by an expert can introduce bias. To address this, a statistical model-assisted method was developed to identify amyloid-containing biopsies and classify amyloidosis subtypes. This method successfully identified novel amyloid-associated proteins and demonstrated the unbiased and reliable classification of amyloid deposits and subtype using mass spectrometry-based data.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Applied
Wisse Hermans, Sabrina Geisslitz, Yamina De Bondt, Niels A. Langenaeken, Katharina A. Scherf, Christophe M. Courtin
Summary: This study used laser microdissection and nanoLC-MS/MS to explore the relative differences in protein composition between different parts of wheat endosperm. The results showed that the sub-aleurone contained a higher proportion of gluten proteins than the inner endosperm, with differences in specific protein components.
Article
Biochemical Research Methods
Dahang Yu, Zhe Wang, Kellye A. Cupp-Sutton, Yanting Guo, Qiang Kou, Kenneth Smith, Xiaowen Liu, Si Wu
Summary: A top-down TMT MS platform for confidently identifying and quantifying low molecular weight intact proteoforms in complex biological samples was developed by combining filter-SEC technique with high-performance size exclusion chromatography. This technique enables high-throughput analysis of intact proteoforms from Escherichia coli cell lysates, representing the first high-throughput TMT labeling-based, quantitative, top-down MS analysis suitable for complex biological samples.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Clinical Neurology
Dominique F. Leitner, Evgeny Kanshin, Arline Faustin, Manon Thierry, Daniel Friedman, Sasha Devore, Beatrix Ueberheide, Orrin Devinsky, Thomas Wisniewski
Summary: Alzheimer's disease (AD) and epilepsy are reciprocally related, with clinical seizures occurring in 10-22% of sporadic AD patients and cognitive deficits occurring in most epilepsy patients. There are common neurophysiological and molecular mechanisms in AD and epilepsy, including pathological changes in the choroid plexus that contribute to synaptic dysfunction.
FRONTIERS IN NEUROLOGY
(2023)
Article
Neurosciences
Amanda M. Canto, Alexandre H. B. Matos, Alexandre B. Godoi, Andre S. Vieira, Beatriz B. Aoyama, Cristiane S. Rocha, Barbara Henning, Benilton S. Carvalho, Vinicius D. B. Pascoal, Diogo F. T. Veiga, Rovilson Gilioli, Fernando Cendes, Iscia Lopes-Cendes
Summary: Research using a multi-omics approach in an animal model of mesial temporal lobe epilepsy revealed differences in the transcriptomic and proteomic profiles between the dentate gyrus (DG) and Cornu Ammonis 3 (CA3) of the hippocampus, suggesting enhanced epileptogenesis in the CA3 region and abnormalities mainly occurring in CA3. Abnormal regulation of excitatory neuronal mechanisms mediated by NMDA receptors, changes in serotonin signaling, and neuronal activity controlled by CaMK regulation and LRRK2/WNT signaling pathways are involved in the epileptogenesis in the pilocarpine model.
Article
Biochemical Research Methods
Yoonsung Joh, Kangbae Lee, Hyunwoo Kim, Heejin Park
Summary: A novel approach, called progressive search, efficiently obtains analysis results for updated databases in tandem mass spectrometry. Compared to performing a normal search from scratch, progressive search achieves the same results much faster.
BMC BIOINFORMATICS
(2023)
Article
Chemistry, Analytical
Daoyang Chen, Zhichang Yang, Xiaojing Shen, Liangliang Sun
Summary: Top-down proteomics (TDP) is an ideal approach for deciphering the histone code and requires new analytical tools with high-capacity separation and highly sensitive detection of proteoforms. In this study, capillary zone electrophoresis (CZE) -MS/MS was used to identify a large number of histone proteoforms with higher sensitivity compared to traditional methods.
ANALYTICAL CHEMISTRY
(2021)
Article
Nutrition & Dietetics
Sarah Brajkovic, Nils Rugen, Carlos Agius, Nicola Berner, Stephan Eckert, Amirhossein Sakhteman, Claus Schwechheimer, Bernhard Kuster
Summary: Plants are crucial for sustainable global food supply, but the understanding of crop proteomes is limited. The presence of secondary metabolites in crop plants has hindered proteomic analyses, requiring individually optimized protein extraction protocols. In this study, a universal protein extraction protocol combined with an automated SP3 protocol and optimized micro-LC-MS/MS conditions was developed for high-quality proteomic analysis of crop plants. The workflow was successfully applied to analyze the proteomes of mature tomato fruits, demonstrating its robustness and potential for large-scale projects mapping crop tissue proteomes.
Article
Urology & Nephrology
Ming Ke, Xin Li, Lin Wang, Shuling Yue, Beibei Zhao
Summary: A proteomic data interpretation procedure for LMD-MS based amyloidosis typing was successfully established, which has a high practicability in clinical application.
Article
Biochemical Research Methods
Fanny C. Liu, Mark E. Ridgeway, Christopher A. Wootton, Alina Theisen, Erin M. Panczyk, Florian Meier, Melvin A. Park, Christian Bleiholder
Summary: Top-down proteomics analyzes intact proteins by their intact mass and fragmentation pattern in tandem mass spectrometry (MS/MS) experiments. Hybrid ion mobility spectrometry-mass spectrometry (IM/MS) methods have gained attention for top-down analysis, improving signal/noise and dynamic range. This study explores a top-down method that combines tandem-trapped ion mobility spectrometry/mass spectrometry (tandem-TIMS/MS) with UV photodissociation (UVPD) and parallel-accumulation serial fragmentation (PASEF) MS/MS analysis. The coupling of these workflows allows for native top-down protein analysis with improved resolution and automated spectra recording.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)