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- The extracellular matrix (ECM) is a complex and dynamic meshwork of proteins providing structural support to cells. It also provides biochemical signals governing cellular processes, including proliferation, adhesion, and migration. Alterations of ECM structure and/or composition have been linked to many pathological processes, including cancer and fibrosis. Over the past decade, mass-spectrometry-based proteomics has become the state-of-the-art method to profile the protein composition of ECMs. However, existing methods do not fully capture the broad dynamic range of protein abundances in […]
- Phytophthora plant pathogens rely on motile biflagellated zoospores to efficiently locate and colonise host tissues. While rhizospheric signals guiding zoospore movement toward roots are known, the protein composition of membranes mediating these responses remains unclear. Here, we used liquid chromatography with tandem mass spectrometry (LC-MS/MS) and proteomic data mining to analyse membrane fractions from the flagella and cell bodies of Phytophthora parasitica zoospores. Major classes of membrane proteins (receptors, transporters and enzymes) were identified and their subcellular distribution between flagella […]
- Publication date: Available online 28 March 2025Source: Journal of Chromatography BAuthor(s): Dimitrios Tsikas
- Would you believe you could sample single cells directly off a plate and lyse/digest and transfer that cell with virtually no losses? No? Sounds sort of unbelievable and there is some "extraordinary claims require some amazing evidence" or something. Would you believe over 3,000 proteins per single cell with a TIMSTOF Pro 1 system running a 21 minute active gradient on those same cells? No? Would that immediatley make you think -wow – that should have ultra super fucking amazingly extraordinary goddamned evidence […]
- Analytical ChemistryDOI: 10.1021/acs.analchem.4c04676
- Analytical ChemistryDOI: 10.1021/acs.analchem.4c06994
- Mass spectrometry (MS)-based proteomics focuses on identifying and quantifying peptides and proteins in biological samples. Processing of MS-derived raw data, including deconvolution, alignment, and peptide-protein prediction, has been achieved through various software platforms. However, the downstream analysis, including quality control, visualizations, and interpretation of proteomics results remains challenging due to the lack of integrated tools to facilitate the analyses. To address this challenge, we developed QuickProt, a series of Python-based Google Colab notebooks for analyzing data-independent acquisition (DIA) and parallel […]
- The unprecedented speed and sensitivity of mass spectrometry (MS) unlocked large-scale applications of proteomics and even enabled proteome profiling of single cells. However, this fast-evolving field is hindered by a lack of scalable dimensionality reduction tools that can compensate for substantial batch effects and missingness across MS runs. Therefore, we present omicsGMF, a fast, scalable, and interpretable matrix factorization method, tailored for bulk and single-cell proteomics data. Unlike current workflows that sequentially apply imputation, batch correction, and principal component analysis, […]
- In evolutionary time, aquatic crustaceans colonized land and faced new terrestrial predators such as spiders and ants. Working with the crustacean woodlouse Porcellio scaber, we tested the hypothesis that the shift from aquatic to terrestrial habitat prompted the evolution of defensive metabolites against terrestrial predators. When attacked by a predator, P. scaber woodlice expel proteinaceous secretions from their tegumental glands. Analyses of gland secretion extracts by gas chromatography-mass spectrometry and by liquid-chromatography-tandem mass spectrometry revealed four metabolites: methyl 8-hydroxy-quinoline-2-carboxylate, methyl […]
- Journal of Mass Spectrometry, Volume 60, Issue 4, April 2025.
- Publication date: Available online 26 March 2025Source: Clinica Chimica ActaAuthor(s): Zhizheng Li, Zhonggan Jin, Ming Zong
- This work is based on the development and optimization of a pressurized liquid extraction method to obtain extracts from peanut shells with the highest possible amount/number of bioactive compounds, mainly flavonoids, with senolytic activity and antioxidant capacity. To achieve optimal extraction conditions, a design of experiments approach was employed to perform a limited and relatively reduced number of experiments. The extracts were consecutively analyzed by methods adapted to the peanut shell matrix to determine antioxidant capacity, total flavonoids, and total […]
- Publication date: Available online 26 March 2025Source: International Journal of Mass SpectrometryAuthor(s): Amir Fayyaz, Muhammad Aslam Baig, Rizwan Ahmed, Muhammad Waqas
- Okay – so this is really cool as a user – even if I feel like I'd only ever use it to look at someone else's data because I don't think I meet the minimum requirements to share my data. Getting an account and digging through the example data is really intuitive. I'm all about more transparency and so it goes here. Maybe I'm sleepy and moving fast but when we get to a bunch of prompts to install my docker […]
- WHOOOOOOOOOOOOOOOOOOOOOOOOOOOOOAAAAAAAA!!!!!Dataset for reanalysis alert!! Mann lab optimized perchlorate based enrichment to get a super cheap sample prep method giving them about 2,000 proteins per sample in human plasma. Then did 36,000 of them?!?! No nanoparticles? Off the shelf stuff? I need to read this, but – whoa.
- Thoracic aortopathies are life-threatening diseases including aneurysm, dissection, and rupture. Phosphodiesterases (PDEs) regulate intracellular cyclic nucleotide concentrations. Recent studies report the influences of cilostazol, a PDE3 inhibitor, and sildenafil, a PDE5 inhibitor, on abdominal aortic aneurysm formation. However, their impacts on thoracic aortopathy remain unknown. In this study, we investigated whether cilostazol and sildenafil affect thoracic aortopathy induced by {beta}-aminopropionitrile (BAPN) administration in mice. Bulk RNA sequencing analysis revealed that BAPN administration upregulated Pde3a transcription in the ascending aorta and […]
- Artificial intelligence stuff has come so far in such a short time. Just last year, a sick 3 year old and I could not get either of the ones I pay for to generate an image of a turtle swimming in ketchup. And – today? Check that out! Totally did it! The future is now! Okay – so in what might possibly be slightly more useful – what about a killer session at ABRF 2025 on AI in proteomics? This featured […]
- Publication date: Available online 26 March 2025Source: Analytica Chimica ActaAuthor(s): Žiga Tkalec, Štěpán Koudelka, Jana Klánová, Elliott J. Price
- European Journal of Mass Spectrometry, Ahead of Print. Rimegepant is a calcitonin gene-related peptide receptor antagonist that has been licensed for migraine headache treatment in the United States, the European Union, the United Kingdom, Hong Kong, Australia, and Kuwait. The oxidation stress study of the …
- HIV-1 exploits host cell post-translation modifications (PTMs) to facilitate production of infectious particles. These modifications include SUMOylation, a dynamically regulated PTM involving covalent attachment of small ubiquitin-like modifiers (SUMOs) to lysine (K) residues of target proteins. SUMOylation modulates the activity of thousands of proteins and multiple fundamental host cellular processes, including pathways hijacked by HIV-1 to promote infection and spread. The SUMOylation of several proteins during HIV-1 infection has been characterized. However, the broad effects of HIV-1 infection on the […]
- Designing stable hetero-oligomeric protein complexes with defined inter-subunit stoichiometries remains a significant challenge. In this study, we report the design of a highly selective heterotrimeric assembly derived from the well-known foldon homotrimer. We generated an aab heterotrimer by introducing the Q11E modification to destabilize the homotrimer and a compensatory modification, either V14A or V14L, to stabilize the hydrophobic core of the heterotrimer. Native mass spectrometry (MS) was essential for guiding the design process, enabling precise characterization of oligomeric states and […]
- As a synthetic polymer, methoxy-polyethylene glycol propionic acid (M-PEG-PA) is widely used in the biomedicine field. Unraveling the pharmacokinetic behavior of M-PEG6-PA in vivo is crucial for evaluating the safety and efficiency of M-PEG-PA-related polymers or drug delivery systems. A high-throughput and green ultra-performance convergence chromatography-tandem mass spectrometry (UPC2-MS/MS) assay was firstly developed and validated for the determination of M-PEG6-PA polymers in a biological matrix. The MRM transition (mass to charge ratio, precursor ions→fragment ions) of m/z 367.2→118.9 was used to quantify M-PEG6-PA […]
- The protein complex cohesin encircles the sister chromatids in early mitosis. At anaphase onset, sister separation is triggered by cleavage of the cohesin subunit SCC1/RAD21 by the cysteine protease separase. SCC1 contains two cleavage sites, where cleavage is stimulated by SCC1 phosphorylation. The molecular mechanisms of substrate recognition and cleavage are only partly understood. Here, we determined a series of cryoEM structures of human separase in apo- or substrate-bound forms that, together with biochemical analysis, provide novel insights into the […]
- C-Terminal cyclic imides are posttranslational modifications on proteins that are recognized and removed by the E3 ligase substrate adapter cereblon (CRBN). Despite the observation of these modifications across the proteome by mass spectrometry-based proteomics, an orthogonal and generalizable method to visualize the C-terminal cyclic imide would enhance detection, sensitivity, and throughput of endogenous CRBN substrate characterization. Here we develop an antibody-like reagent, termed cerebody, for visualizing and enriching C-terminal cyclic imide-modified proteins. We describe the engineering of CRBN derivatives to […]
- J. Anal. At. Spectrom., 2025, Accepted ManuscriptDOI: 10.1039/D5JA00009B, Paper Open Access   This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.Benjamin T Manard, Sarah Szakas, Jordan Stanberry, Brian W. Ticknor, Leslie O'Brien, Mark Boris, Josh Hewitt, Paula Cable-Dunlap, Hunter B. AndrewsLaser ablation – inductively coupled plasma – time of flight – mass spectrometry (LA-ICP-TOF-MS) was employed to rapidly analyze environmental particle samples collected using aerosol contaminate extractors (ACE). The ACE…The content of this RSS Feed (c) The […]