Mammalian Genome, Год журнала: 2024, Номер unknown
Опубликована: Дек. 30, 2024
Язык: Английский
Journal of Proteome Research, Год журнала: 2024, Номер 23(2), С. 857 - 867
Опубликована: Янв. 17, 2024
Membrane proteins, particularly those on the cell surface, play pivotal roles in diverse physiological processes, and their dysfunction is linked to a broad spectrum of diseases. Despite being crucial biomarkers therapeutic drug targets, low abundance hydrophobic nature pose challenges isolation quantification, especially when extracted from tissues organs. To overcome these hurdles, we developed membrane-mimicking peptidisc, enabling membrane proteome water-soluble library conducive swift identification through liquid chromatography with tandem mass spectrometry. This study applies method across five mice organs, capturing between 200 450 plasma proteins each case. More than just protein identification, peptidisc used estimate relative linking cell-surface molecular functions organ biological roles, thereby contributing ongoing discourse specificity. contribution holds substantial potential for unveiling new avenues exploration downstream applications involving knowledge proteome.
Язык: Английский
Процитировано
10
The EMBO Journal, Год журнала: 2023, Номер 42(23)
Опубликована: Ноя. 2, 2023
Substantial efforts are underway to deepen our understanding of human brain morphology, structure, and function using high-resolution imaging as well high-content molecular profiling technologies. The current work adds these approaches by providing a comprehensive quantitative protein expression map 13 anatomically distinct regions covering more than 11,000 proteins. This was enabled the optimization, characterization, implementation high-sensitivity high-throughput microflow liquid chromatography timsTOF tandem mass spectrometry system (LC-MS/MS) capable analyzing 2,000 consecutive samples prepared from formalin-fixed paraffin embedded (FFPE) material. Analysis this proteomic resource highlighted region-enriched patterns functional classes, localization differences between individual markers for specific areas. To facilitate access ease further mining data scientific community, all can be explored online in purpose-built R Shiny app (https://brain-region-atlas.proteomics.ls.tum.de).
Язык: Английский
Процитировано
15
Journal of Nuclear Medicine, Год журнала: 2025, Номер unknown, С. jnumed.124.268699 - jnumed.124.268699
Опубликована: Янв. 2, 2025
Microglia, the immune cells in brain, play a significant role pathophysiology of neurodegenerative diseases. To visualize these living we developed PET ligand, [11C]NCGG401 (4-{2-[((1R,2R)-2-hydroxycyclohexyl)(methyl)amino]benzothiazol-6-yloxy}-N-methylpicolinamide, NCGG401), that targets colony-stimulating factor 1 receptor (CSF1R). In this study, present first-in-human evaluation to assess its safety profile and then evaluate kinetics quantify CSF1R human brain. Methods: Head upper thigh scans were conducted 3 healthy men estimate effective dose [11C]NCGG401. Brain performed on 6 men, combined with arterial blood sampling metabolite analyses. Compartmental graphical models used data indirectly compared regional protein levels after death reported proteomics study. addition, results study directly imaging 18-kDa translocator using [11C]DPA-713 (N,N-diethyl-2-[2-(4-methoxyphenyl)-5,7-dimethylpyrazolo[1,5-a]pyrimidin-3-yl]acetamide, DPA-713). Results: The administration did not result severe adverse events. doses per injected activity 5.1 ± 0.2 µSv/MBq for 6.1 0.3 women. demonstrated good brain permeability, peak uptake reaching an SUV 3. Regional total distribution volumes reliably quantified 2-tissue compartment model Logan plot 60 min scan data. resulting parametric images reflected known Furthermore, volume values showed correlation levels. distributions different from those [11C]DPA-713. Conclusion: appear reflect microglia-specific consistent findings by others. However, ultimate confirmation specific binding should be validated evaluating, suitable preclinical or experiments, pharmacologic blockade in vivo.
Язык: Английский
Процитировано
0
Journal of Molecular Biology, Год журнала: 2025, Номер unknown, С. 169008 - 169008
Опубликована: Фев. 1, 2025
Язык: Английский
Процитировано
0
Journal of Proteome Research, Год журнала: 2025, Номер unknown
Опубликована: Март 7, 2025
Mass spectrometry (MS)-based proteomics relies heavily on MS/MS (MS2) data, which do not fully exploit the available MS1 information. Traditional peptide identity propagation (PIP) methods, such as match-between-runs (MBR), are limited to similar runs, particularly with same liquid chromatography (LC) gradients, thus potentially underutilizing libraries. We introduce SWAPS, a novel and modular MS1-centric framework incorporating advances in property prediction, extensive libraries, deep-learning-based postprocessing enable explore PIP across more diverse experimental conditions LC gradients. SWAPS substantially enhances precursor identification, especially shorter On example of 30, 15, 7.5 min achieves increases 46.3, 86.2, 112.1% level over MaxQuant's MS2-based identifications. Despite inherent challenges controlling false discovery rates (FDR) MS1-based demonstrates strong efficacy deconvoluting signals, offering powerful discrimination deeper sequence exploration, while maintaining quantitative accuracy. By building applying predictions practical contexts, reveals that current models, advanced, still comparable measurements, sparking need for further research. Additionally, its design allows seamless integration future improvements, positioning forward-looking tool proteomics.
Язык: Английский
Процитировано
0
ACS Omega, Год журнала: 2025, Номер unknown
Опубликована: Март 17, 2025
The efforts to utilize microflow liquid chromatography hyphenated tandem mass spectrometry (μLC-MS/MS) for deep-scale proteomic analysis are still growing. In this work, two-dimensional LC separation and peptide derivatization by a tag (TMT) were used assess the capability of μLC-MS/MS reveal protein changes associated with severe chronic anthracycline cardiotoxicity phenotype in comparison nanoflow (nLC-MS/MS). control anthracycline-treated rabbit myocardium nLC-MS/MS allowed quantification 3956 4549 proteins, respectively, 84% these proteins shared both data sets. Both revealed marked global proteome dysregulation cardiotoxicity, significant change approximately 55% all detected proteins. less compressed more precise determination TMT channel ratio correspondingly broader fold-change distribution than nLC-MS/MS. total number significantly changed was higher (2498 vs 2183, 1900 shared), whereas opposite true cutoff ≥ 2 (535 820). profound concerned mainly cardiomyocyte sarcomeres, costameres, intercalated discs, mitochondria, extracellular matrix. addition, distinct alterations immune defense response found remarkable involvement type I interferon signaling that has been recently hypothesized be essential pathogenesis. Hence, sound alternative can useful comprehensive mapping myocardial such as those cardiotoxicity.
Язык: Английский
Процитировано
0
The American Journal of Human Genetics, Год журнала: 2025, Номер unknown
Опубликована: Апрель 1, 2025
The post-transcriptional modification of tRNAs plays a crucial role in tRNA structure and function. Pathogenic variants tRNA-modification enzymes have been implicated wide range human neurodevelopmental neurological disorders. However, the molecular basis for many these disorders remains unknown. Here, we describe comprehensive cohort 43 individuals from 31 unrelated families with bi-allelic methyltransferase 1 (TRMT1). These present disorder universally characterized by developmental delay intellectual disability, accompanied variable behavioral abnormalities, epilepsy, facial dysmorphism. identified include ultra-rare TRMT1 variants, comprising missense predicted loss-of-function which segregate observed clinical pathology. Our findings reveal that several lead to mis-splicing consequent loss protein accumulation. Moreover, cells derived harboring exhibit deficiency modifications catalyzed TRMT1. Molecular analysis reveals distinct regions required activity binding. Notably, depletion Trmt1 zebrafish is sufficient induce phenotypes along gene-expression changes associated disrupted cell cycle, immune response, neurodegenerative Altogether, demonstrate TRMT1-catalyzed leads disability provides insight into underpinnings caused pathogenic variants.
Язык: Английский
Процитировано
0
The EMBO Journal, Год журнала: 2024, Номер 44(1), С. 304 - 329
Опубликована: Ноя. 18, 2024
Язык: Английский
Процитировано
3
Cell Reports Medicine, Год журнала: 2024, Номер 5(12), С. 101843 - 101843
Опубликована: Дек. 1, 2024
Язык: Английский
Процитировано
3
Analytical Chemistry, Год журнала: 2024, Номер 96(33), С. 13358 - 13370
Опубликована: Авг. 5, 2024
Formalin-fixed paraffin-embedded (FFPE) tissues are suitable for proteomic and phosphoproteomic biomarker studies by data-independent acquisition mass spectrometry. The choice of the sample preparation method influences number, intensity, reproducibility identifications. By comparing four deparaffinization rehydration methods, including heptane, histolene, SubX, xylene, we found that heptane methanol produced lowest coefficients variation (CVs). Using this, five extraction methods from literature were modified evaluated their performance using kidney, leg muscle, lung, testicular rat organs. All performed well, except SP3 due to insufficient tissue lysis. Heat n' Beat was fastest most reproducible with highest digestion efficiency CVs. S-Trap peptide yield, while TFE best phosphopeptide enrichment efficiency. quantitation FFPE-derived peptides remains an ongoing challenge bias in UV fluorescence assays across notably SPEED. Functional analysis demonstrated each favored extracting some gene ontology cellular components over others chromosome, cytoplasmic, cytoskeleton, endoplasmic reticulum, membrane, mitochondrion, nucleoplasm protein groups. outcome is a set recommendations choosing appropriate different settings.
Язык: Английский
Процитировано
2