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)
Review
Medicine, General & Internal
Sarah R. Weber, Yuanjun Zhao, Christopher Gates, Jingqun Ma, Felipe da Veiga Leprevost, Venkatesha Basrur, Alexey I. Nesvizhskii, Thomas W. Gardner, Jeffrey M. Sundstrom
Summary: Vitreous fluid has emerged as a valuable medium for studying retinal diseases, with proteomic analysis providing insights into proliferative diabetic retinopathy. Despite the lack of standardized methodology, there have been numerous studies utilizing mass spectrometry for vitreous proteomic analysis. Moving forward, addressing common pitfalls and proposing next steps is crucial for advancing this field.
JOURNAL OF CLINICAL MEDICINE
(2021)
News Item
Multidisciplinary Sciences
Ewen Callaway
Summary: Microbial molecules from soil, seawater, and human bodies are among the least understood substances on Earth.
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
Paleerath Peerapen, Wanida Boonmark, Visith Thongboonkerd
Summary: In this study, the interacting complexes of the apical membrane (ApANXA1) and cytosolic (cyANXA1) forms of ANXA1 in renal epithelial cells under high-calcium condition were characterized using proteomic and bioinformatic approaches. The results showed that the interacting proteins had both common and unique characteristics and properties. This study provides insights into the biochemistry, functions, and pathophysiology of CaOx kidney stone formation induced by high-calcium condition.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemical Research Methods
Devon Kohler, Mateusz Staniak, Tsung-Heng Tsai, Ting Huang, Nicholas Shulman, Oliver M. Bernhardt, Brendan X. MacLean, Alexey I. Nesvizhskii, Lukas Reiter, Eduard Sabido, Meena Choi, Olga Vitek
Summary: The MSstats R-Bioconductor family of packages, particularly the new version MSstats v4.0, is widely used for statistical analyses of quantitative proteomic experiments. It provides improved usability, versatility, and accuracy of statistical methodology, as well as better memory use and computation speed. Empirical comparisons have demonstrated the stronger performance and better usability of MSstats v4.0 compared to existing methods.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Valeria C. Nogueira, Valzimeire do N. de Oliveira, Maria I. F. Guedes, Bradley J. Smith, Jose E. da C. Freire, Nidyedja G. G. Gonsalves, Ana C. de O. M. Moreira, Renato de A. Moreira
Summary: This study identified differentially expressed proteins in the serum of T1D patients using LC-MS/MS analysis, and found that these proteins are associated with the immune system, inflammation, and growth hormone stimulus response. The results suggest that these proteins could be potential targets for future investigations and validation of protein biomarkers in T1D.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Cell Biology
Paul Dowling, Dieter Swandulla, Kay Ohlendieck
Summary: This review discusses the main bioanalytical methods used in the proteomic characterization of skeletal muscle tissues and the impact of skeletal muscle proteomics on whole-body physiology. Mass spectrometric studies have greatly improved our understanding of protein diversity and muscle tissue, which can be integrated with other omics-type methods to establish a systems biology view of skeletal muscle function.
Review
Biochemical Research Methods
Zainab Noor, Seong Beom Ahn, Mark S. Baker, Shoba Ranganathan, Abidali Mohamedali
Summary: Accurate protein identification is crucial in proteomics, with mass spectrometry being the primary technique used. Understanding data generation and parameters used in computational tools is essential for proper protein identification. Bioinformatics and computational methodologies are also important for validating protein identification in proteomics.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Microbiology
Yeva Mirzakhanyan, Andris Jankevics, Richard A. Scheltema, Paul David Gershon
Summary: Through the combination of deep learning and cross-linking mass spectrometry, an atomic-level model and an integrated processing/assembly pathway for a structural component of the vaccinia virion, protein P4a, has been established. Proteolytic separation of the C-terminal P4a-3 segment triggers a conformational rotation within the N-terminal P4a-1 segment, which is fixed by disulfide-locking and removes a steric block to trimerization of the processing intermediate P4a-1+2. These events lead to the proteolytic separation of P4a-2 and allow the assembly of P4a-1 into a hexagonal lattice enclosing the nascent virion core.
Article
Health Care Sciences & Services
Oxana P. Trifonova, Dmitry L. Maslov, Elena E. Balashova, Steven Lichtenberg, Petr G. Lokhov
Summary: Diabetic nephropathy is a common complication of diabetes that requires early diagnosis. Using metabolomics analysis, researchers identified a combination of 15 compounds that showed high accuracy in diagnosing DN, particularly in the late stage, with a diagnostic performance of up to 99%.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Genetics & Heredity
Bo Li, Xu Zhao, Wanrun Xie, Zhenzhen Hong, Yi Zhang
Summary: Diabetic nephropathy (DN) is a common complication of diabetes and a major cause of kidney disease. Although significant progress has been made in understanding the etiopathogenesis of DN, the genetic mechanisms underlying these effects remain unknown.
FRONTIERS IN GENETICS
(2023)
Article
Biology
Matthias Fahrner, Melanie Christine Foll, Bjorn Andreas Gruning, Matthias Bernt, Hannes Rost, Oliver Schilling
Summary: The integration of an open-source DIA analysis suite in the web-based and user-friendly Galaxy framework, along with comprehensive training materials, enables a wide community of researchers to perform reproducible and transparent DIA data analysis.
Article
Biochemical Research Methods
Sebastian Dorl, Stephan Winkler, Karl Mechtler, Viktoria Dorfer
Summary: Spectral library search enables more sensitive peptide identification in tandem mass spectrometry experiments, but suffers from limited availability of high-quality libraries and the difficulty of creating decoy spectra for result validation. MS Ana is a new spectral library search engine that addresses these issues by allowing the use of curated or predicted libraries and providing robust false discovery control through its own decoy library generation algorithm. In benchmark tests, MS Ana outperformed database search, achieving 36% more spectrum matches and 4% more proteins identified in single-shot human cell-line data. The quality of result validation was demonstrated through tests on synthetic peptide pools, and the importance of library selection was highlighted by comparing the performance of different publicly available human spectral libraries.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Rosalie G. J. Rietjens, Gangqi Wang, Anouk I. M. van der Velden, Angela Koudijs, M. Cristina Avramut, Sander Kooijman, Patrick C. N. Rensen, Johan van der Vlag, Ton J. Rabelink, Bram Heijs, Bernard M. van den Berg
Summary: Diabetes is a major risk factor for kidney disease, with diabetic nephropathy occurring in almost half of all diabetic patients. Metabolism has been found to play a crucial role in determining cell fate and repair. Mass spectrometry imaging was used to identify specific metabolic dysregulation in different tissues in order to understand the early metabolic changes in renal cell types caused by diabetes.
SCIENTIFIC REPORTS
(2023)
Article
Allergy
Kristin C. Sokol, Neil K. Amar, Jonathan Starkey, J. Andrew Grant
ANNALS OF ALLERGY ASTHMA & IMMUNOLOGY
(2013)
Article
Neurosciences
Larry A. Denner, Jennifer Rodriguez-Rivera, Sigmund J. Haidacher, Jordan B. Jahrling, J. Russ Carmical, Caterina M. Hernandez, Yingxin Zhao, Rovshan G. Sadygov, Jonathan M. Starkey, Heidi Spratt, Bruce A. Luxon, Thomas G. Wood, Kelly T. Dineley
JOURNAL OF NEUROSCIENCE
(2012)
Article
Neurosciences
Miroslav N. Nenov, Fernanda Laezza, Sigmund J. Haidacher, Yingxin Zhao, Rovshan G. Sadygov, Jonathan M. Starkey, Heidi Spratt, Bruce A. Luxon, Kelly T. Dineley, Larry Denner
JOURNAL OF NEUROSCIENCE
(2014)
Article
Critical Care Medicine
Ping Wu, Yingxin Zhao, Sigmund J. Haidacher, Enyin Wang, Margaret O. Parsley, Junling Gao, Rovshan G. Sadygov, Jonathan M. Starkey, Bruce A. Luxon, Heidi Spratt, Douglas S. DeWitt, Donald S. Prough, Larry Denner
JOURNAL OF NEUROTRAUMA
(2013)
Article
Biochemical Research Methods
Rovshan G. Sadygov, Yingxin Zhao, Sigmund J. Haidacher, Jonathan M. Starkey, Ronald G. Tilton, Larry Denner
JOURNAL OF PROTEOME RESEARCH
(2010)
Article
Multidisciplinary Sciences
Jonathan M. Starkey, Yingxin Zhao, Rovshan G. Sadygov, Sigmund J. Haidacher, Wanda S. LeJeune, Nilay Dey, Bruce A. Luxon, Maureen A. Kane, Joseph L. Napoli, Larry Denner, Ronald G. Tilton
Article
Multidisciplinary Sciences
Benjamin B. Gelman, Tiansheng Chen, Joshua G. Lisinicchia, Vicki M. Soukup, J. Russ Carmical, Jonathan M. Starkey, Eliezer Masliah, Deborah L. Commins, Dianne Brandt, Igor Grant, Elyse J. Singer, Andrew J. Levine, Jeremy Miller, Jessica M. Winkler, Howard S. Fox, Bruce A. Luxon, Susan Morgello
Article
Endocrinology & Metabolism
JM Starkey, SJ Haidacher, WS LeJeune, X Zhang, BC Tien, S Choudhary, AR Brasier, LA Denner, RG Tilton
