Article
Biochemistry & Molecular Biology
Olga Kunyayskaya, Alla Mikheenko, Alexey Gurevich
Summary: This study presents NPvis, a visualizer for evaluating PNP-MS/MS matches. The tool allows researchers to assess the correctness of the matches by mapping annotated spectrum peaks to corresponding PNP fragments. It works even if the exact chemical structure of the matching PNP is unknown.
Article
Multidisciplinary Sciences
Yuliya Korolkova, Alexander Mikov, Anna Lobas, Elizaveta Solovyeva, Alexey Surin, Yaroslav Andreev, Mikhail Gorshkov, Sergey Kozlov
Summary: This study conducted transcriptome and proteome analysis on the venom of Tibellus oblongus spider, revealing the presence of several new toxins.
Article
Biochemistry & Molecular Biology
Ahmad Jalloh, Antwoine Flowers, Charles Hudson, Dale Chaput, Jennifer Guergues, Stanley M. Stevens, Paula C. Bickford
Summary: Research indicates that microglial activity is a central factor in aging-related dysfunction, with protein signaling cascades playing a key role in altering microglial function. Polyphenols may offer a means of addressing age-related decline, highlighting their potential therapeutic role in age-associated dysfunction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Valeriy I. I. Postoenko, Leyla A. A. Garibova, Lev I. I. Levitsky, Julia A. A. Bubis, Mikhail V. V. Gorshkov, Mark V. V. Ivanov
Summary: One of the key steps in DDA proteomics is detecting peptide isotopic clusters and matching them to MS/MS-based peptide identifications. IQMMA is an integrated solution that combines multiple untargeted peptide feature detection algorithms to provide the most probable intensity values for the MS/MS-based identifications.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Guillaume Postic, Jessica Andreani, Julien Marcoux, Victor Reyss, Raphael Guerois, Julien Rey, Emmanuelle Mouton-Barbosa, Yves Vandenbrouck, Sarah Cianferani, Odile Burlet-Schiltz, Gilles Labesse, Pierre Tuffery
Summary: Proteo3Dnet is a web server dedicated to analyzing mass spectrometry interactomics experiments by searching for structurally interacting molecules, short linear motifs, and physically validated protein-protein interactions, providing a clearer overview of the data. The server returns a graph of identified interactions that can be interactively explored to understand core complexes and suggest undetected partners.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Analytical
Mu Lin, Jixin Qiao, Xiaolin Hou, Robin Golser, Karin Hain, Peter Steier
Summary: Background check and dust control measures significantly improved the procedure blanks and detection limits for U-236 and U-233, with analytical precision relying on AMS counting statistics in the analyses of environmental-level long-lived radionuclides conducted in former or active nuclear facilities.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Kevin A. Kovalchik, Qing Ma, Laura Wessling, Frederic Saab, Jerome D. Duquette, Peter Kubiniok, David J. Hamelin, Pouya Faridi, Chen Li, Anthony W. Purcell, Anne Jang, Eustache Paramithiotis, Marco Tognetti, Lukas Reiter, Roland Bruderer, Joel Lanoix, Mathieu Courcelles, Pierre Thibault, Etienne Caron, Isabelle Sirois
Summary: Researchers have developed a semi-automated quality control software tool called MhcVizPipe (MVP) for rapid assessment of multiple MHC class I and II immunopeptidomic datasets generated by mass spectrometry. MVP provides a quick and comprehensive view of sample quality, composition, and MHC specificity to accelerate the decision-making process for data interpretation.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemical Research Methods
Chi-Hua Lee, Jack C. Tang, Nathan G. Hendricks, Bahman Anvari
Summary: This study compared the differences in the proteomes of nano- and micro-sized erythrocyte ghosts with normal RBCs. It was found that the relative abundances of mechano-modulatory proteins and immunomodulatory proteins were higher in the nano-sized particles.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Olatomiwa O. Bifarin, Samyukta Sah, David A. Gaul, Samuel G. Moore, Ruihong Chen, Murugesan Palaniappan, Jaeyeon Kim, Martin M. Matzuk, Facundo M. Fernandez
Summary: Ovarian cancer is a deadly cancer that affects the female reproductive system and is often asymptomatic until later stages. Little is known about the metabolic changes in the early stages of high-grade serous ovarian cancer. This study used a mouse model and machine learning analysis to examine the temporal changes in serum lipidome. The results showed unique alterations in cell membrane stability, proliferation, and survival during cancer development and progression, providing potential targets for early detection and prognosis of ovarian cancer.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Analytical
Dan B. Kristensen, Martin orgaard, Trine M. Sloth, Nanna S. Christoffersen, Katrine Z. Leth-Espensen, Pernille F. Jensen
Summary: Peptide mapping by LC-MS and the related MAM are commonly used analytical tools in biopharmaceutical development for verifying protein structure and mapping/quantifying modifications or product quality attributes. Traditional proteolytic digestion workflows are labor-intensive, but recently introduced high-temperature automatic workflows have improved robustness and reproducibility. This article presents a modified automatic digestion workflow involving two-step digestion at high and low temperatures, which reduces missed cleavages and improves digestion completeness. Switching from traditional C18 to less retentive C4 column chemistry also reduces peak tailing and carry-over of hydrophobic peptides without compromising MS/MS-derived sequence coverage.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Andrea Laguillo-Gomez, Enrique Calvo, Noa Martin-Cofreces, Marta Lozano-Prieto, Francisco Sanchez-Madrid, Jesus Vazquez
Summary: Open-search methods with prior knowledge improve identification performance of protein post-translational modifications by minimizing experimental errors and precursor mass assignation. The introduction of a novel approach enables the study of a wider variety of PTMs, including unknown or unexpected modifications.
JOURNAL OF PROTEOMICS
(2023)
Article
Biochemistry & Molecular Biology
Ildar T. Gabdrakhmanov, Mikhail V. Gorshkov, Irina A. Tarasova
Summary: The study aims to optimize the statistical threshold and selection of differentially regulated proteins through the analysis of known concentration protein samples and biological models of early and late cellular responses to stress. The research suggests a visual approach using volcano plots and gene ontology analysis to guide researchers in better selecting differentially regulated proteins.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Biochemistry & Molecular Biology
Floriane Pailleux, Pauline Maes, Michel Jaquinod, Justine Barthelon, Marion Darnaud, Claire Lacoste, Yves Vandenbrouck, Benoit Gilquin, Mathilde Louwagie, Anne-Marie Hesse, Alexandra Kraut, Jerome Garin, Vincent Leroy, Jean-Pierre Zarski, Christophe Bruley, Yohann Coute, Didier Samuel, Philippe Ichai, Jamila Faivre, Virginie Brun
Summary: By utilizing bioinformatics and proteomics, this study identified alcohol dehydrogenase 1B (ADH1B) as a potential blood biomarker for acetaminophen-induced acute liver injury (ALI). Serum ADH1B concentration increased significantly during the acute phase of the disease and returned to normal levels during recovery.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Doungdean Tummanatsakun, Tanakorn Proungvitaya, Sittiruk Roytrakul, Siriporn Proungvitaya
Summary: APEX1 is involved in DNA damage repair and is associated with metastasis in several human cancers. Our study suggests that in cholangiocarcinoma, APEX1 may mediate metastasis through CDC42 and SOS1, and high expression levels of APEX1 and its related proteins are correlated with shorter survival times.
Article
Biochemical Research Methods
Yehia Mokhtar Farag, Carlos Horro, Marc Vaudel, Harald Barsnes
Summary: Mass spectrometry-based proteomics generates large amounts of data, and PeptideShaker Online is a user-friendly web-based framework that helps researchers with data identification, storage, and interpretation.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Geriatrics & Gerontology
Melissa Scholefield, Stephanie J. Church, Jingshu Xu, Stefano Patassini, Federico Roncaroli, Nigel M. Hooper, Richard D. Unwin, Garth J. S. Cooper
Summary: The study found alterations in levels of several metals across multiple regions of Parkinson's disease dementia (PDD) brain, with widespread decreases in copper being the most common, closely resembling those in Alzheimer's disease dementia (ADD) patients, suggesting similar disease mechanisms in both dementias.
FRONTIERS IN AGING NEUROSCIENCE
(2021)
Article
Agriculture, Multidisciplinary
Siobhan Mullan, Philippa Wiltshire, Kate Cross, David C. J. Main, Kate Still, Madeleine Crawley, Andrew W. Dowsey
Summary: Animal welfare is a crucial aspect of sustainability in livestock farming, and the introduction of welfare outcome monitoring in the Red Tractor UK national dairy assurance scheme has led to significant improvements in reducing the prevalence of diseases among cows while increasing milk yield per cow.
INTERNATIONAL JOURNAL OF AGRICULTURAL SUSTAINABILITY
(2022)
Article
Ophthalmology
Izabela P. Klaska, Anne White, Pilar Villacampa, Justin Hoke, Laura Abelleira-Hervas, Ryea N. Maswood, Robin R. Ali, Catey Bunce, Richard D. Unwin, Garth J. S. Cooper, Paul N. Bishop, James W. Bainbridge
Summary: Intravitreal administration of recombinant human opticin can safely protect against the development of pathological angiogenesis and promote its regression in mice. This finding suggests the potential use of opticin as a therapeutic intervention for ocular diseases.
EXPERIMENTAL EYE RESEARCH
(2022)
Letter
Multidisciplinary Sciences
Richard D. Unwin, Daniela S. Couto, Simon J. Clark
Article
Geriatrics & Gerontology
Sasha A. Philbert, Jingshu Xu, Melissa Scholefield, Stephanie J. Church, Richard D. Unwin, Garth J. S. Cooper
Summary: Vascular dementia (VaD) is the second most common cause of age-related dementia, and there are currently no disease-modifying therapies available for VaD. A study investigating VaD found elevated levels of sodium and sodium/potassium ratio, as well as decreased levels of potassium in the hippocampal tissue. These findings suggest dysfunction of Na+/K+-exchanging ATPase, possibly due to deficient ATP generation. The study highlights the potential diagnostic importance of measuring cerebral sodium in VaD patients.
FRONTIERS IN AGING NEUROSCIENCE
(2022)
Article
Multidisciplinary Sciences
Selina Mcharg, Laura Booth, Rahat Perveen, Isabel Riba Garcia, Nicole Brace, Nadhim Bayatti, Panagiotis Sergouniotis, Alexander M. Phillips, Anthony J. Day, Graeme C. M. Black, Simon J. Clark, Andrew W. Dowsey, Richard D. Unwin, Paul N. Bishop
Summary: Age-related macular degeneration (AMD) is a major cause of visual loss and is strongly associated with common haplotypes on chromosome 1 (CFH Y402H variant) and chromosome 10 (near HTRA1/ARMS2). In this study, the submacular tissue of older donors with genetic risk but without clinical features of AMD was analyzed using mass spectrometry-based quantitative proteomics. The results showed that the high-risk allele groups on chromosome 1 and chromosome 10 had common protein changes compared to the low-risk group, particularly increased levels of mast cell-specific proteases. Additional histological analyses revealed increased mast cells and denatured collagen in the submacular tissue of donors with genetic risk of AMD but without clinical features, as well as in donors with high-risk chromosome 1 alleles and early AMD. These findings suggest that increased mast cell infiltration, degranulation, and extracellular matrix remodeling are early events in AMD pathogenesis, and represent a mechanistic link between chromosome 1 and chromosome 10-mediated AMD.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Geriatrics & Gerontology
Sasha A. Philbert, Jingshu Xu, Stephanie J. Church, Richard D. Unwin, Federico Roncaroli, Garth J. S. Cooper
Summary: This study used inductively coupled plasma-mass spectrometry to measure the levels of essential metals in vascular dementia (VaD) brain tissue. The results showed elevated sodium levels, decreased potassium levels, and increased Na/K ratios in VaD brain tissue. These findings suggest a possible involvement of altered Na+/K+ exchanging ATPase activity in the pathogenesis of VaD.
FRONTIERS IN AGING NEUROSCIENCE
(2022)
Article
Geriatrics & Gerontology
Crystal Sang, Sasha A. Philbert, Danielle Hartland, Richard. D. Unwin, Andrew W. Dowsey, Jingshu Xu, Garth J. S. Cooper
Summary: Sporadic Alzheimer's disease (sAD) is a common cause of age-related neurodegeneration and dementia. This study suggests that a deficiency of vitamin B5 may impair brain energy metabolism in sAD by affecting the levels of mitochondrial-TCA cycle enzymes.
FRONTIERS IN AGING NEUROSCIENCE
(2022)
Article
Microbiology
Tarcisio Brignoli, Mario Recker, Winnie W. Y. Lee, Tim Dong, Ranjeet Bhamber, Mahableshwar Albur, Philip Williams, Andrew W. Dowsey, Ruth C. Massey
Summary: Staphylococcus aureus bacteraemia (SAB) is a major cause of blood-stream infection (BSI) in both healthcare and community settings. Recent studies have shown the importance of the level of cytolytic toxin production by the infecting bacterium. This study demonstrates that this cytotoxicity can be determined directly from the diagnostic MALDI-TOF mass spectrum.
Article
Immunology
Anna L. Tierney, Wajd Mohammed Alali, Thomas Scott, Karen S. Rees-Unwin, Simon J. Clark, Richard D. Unwin
Summary: The SARS-CoV-2 virus continues to cause significant morbidity and mortality worldwide. Dysregulation of the complement cascade, specifically elevations in FHR proteins, may predict disease severity in COVID-19 patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, General & Internal
Sasha A. Philbert, Sarah J. Schoenberger, Jingshu Xu, Stephanie J. Church, Richard D. Unwin, Garth J. S. Cooper
Summary: The study found that hippocampal copper levels were significantly elevated in patients with T2D, similar to untreated cases of Wilson's disease (WD), while hippocampal copper levels were markedly deficient in patients with sAD. These results suggest that hippocampal copper may play a role in the neurodegeneration and cognitive impairment in T2D, and therapeutic approaches targeting copper reduction, similar to those used in WD, may be applicable to patients with T2D.
Article
Veterinary Sciences
I Chan, A. Dowsey, P. Lait, S. Tasker, E. Blackwell, C. R. Helps, E. N. Barker
Summary: This study investigates the common causes of upper respiratory tract disease (URTD) in cats in the UK pet cat population and the risk factors for their oral carriage. The results showed that out of 430 cats, 9 (2.1%) were positive for feline herpesvirus (FHV), 57 (13.3%) were positive for feline calicivirus (FCV), and 5 (1.2%) were positive for Chlamydia felis. FCV was the most frequently encountered URTD pathogen in this sample of cats, highlighting the importance of appropriate disinfectant choice. Assessment for co-infection with FCV is recommended in cats suspected of having FHV or C. felis infection.
JOURNAL OF SMALL ANIMAL PRACTICE
(2023)
Article
Neurosciences
Sasha A. Philbert, Jingshu Xu, Melissa Scholefield, Stefano Patassini, Stephanie J. Church, Richard D. Unwin, Federico Roncaroli, Garth J. S. Cooper
Summary: Vascular dementia (VaD) is a common type of dementia in the elderly, but its molecular basis is not well understood compared to other age-related dementias. This study used a novel technique to measure urea levels in post-mortem brain tissue and found elevated levels in multiple regions of the brain in VaD cases, suggesting a common urea-mediated disease mechanism present in several types of age-related dementias.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2023)
Article
Chemistry, Analytical
Stephanie Church, Kimme L. Hyrich, Kayode Ogungbenro, Richard D. Unwin, Anne Barton, James Bluett
Summary: We developed a novel HPLC MS/MS assay for the quantification of tofacitinib, which showed the potential to sensitively measure biochemical adherence. This method has the potential to be a more objective measure that could be used in the future in the clinic, but further studies are needed to explore factors that may influence drug level measurement, such as patients' clinical characteristics.
ANALYTICAL METHODS
(2023)