Article
Chemistry, Analytical
Dong Hao Wang, Hui Gyu Park, Zhen Wang, R. J. Scott Lacombe, Vadim V. Shmanai, Andrei Bekish, Karsten Schmidt, Mikhail S. Shchepinov, J. Thomas Brenna
Summary: This study introduces a novel method for quantitatively determining the deuterium content along a hydrocarbon chain. By utilizing deuteration reactions and analysis techniques, the method enables accurate quantification of deuterium abundance at different positions of D-HUFA.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Jonathan Strutz, Kevin M. Shebek, Linda J. Broadbelt, Keith E. J. Tyo
Summary: MINE 2.0 is a significant improvement that utilizes new biochemical transformation rules to increase the database size and improve the matching of unannotated peaks from untargeted metabolomics datasets.
Article
Environmental Sciences
Charlotte Mappa, Olivier Pible, Jean Armengaud, Beatrice Alpha-Bazin
Summary: The use of mass spectrometry for rapid identification of microorganisms has been expanding in recent years due to its efficiency. This methodology is crucial in combating bioterrorism by providing quick and versatile pathogen identification, including subtyping for confirmation of widespread attacks. The study presented a new methodology based on next-generation proteomics and tandem mass spectrometry to discover protein biomarkers for discriminating spores and vegetative cells, with a focus on Bacillus atrophaeus, a biowarfare simulant. The researchers proposed a global quantitative evaluation of discriminant biomarkers for these two groups based on normalized spectral abundance factors.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Chemistry, Analytical
David S. Gertner, Jake P. Violi, David P. Bishop, Matthew P. Padula
Summary: Due to the complexity of lipids, in silico generated spectral libraries have become crucial for identifying lipid species in mass spectral data. However, many existing libraries have limitations in usability and representativeness. To address this issue, we introduce Lipid Spectrum Generator, an open-source tool specifically designed for aiding lipid identification in liquid chromatography-tandem mass spectrometry analysis.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Tyler S. Larson, Thomas J. Diprospero, Gary L. Glish, Matthew R. Lockett
Summary: In this study, a novel method was used to investigate the lipid profile changes in oxaliplatin-sensitive and resistant cells, revealing significant increases in triglycerides and cholesterol esters caused by oxaliplatin, which were correlated with lipid droplet formation.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Ophthalmology
Maite Lopez-Lopez, Uxia Regueiro, Susana Belen Bravo, Maria del Pilar Chantada-Vazquez, Carmen Pena, Elio Diez-Feijoo, Pablo Hervella, Isabel Lema
Summary: This study utilized a qualitative approach to explore the tear proteome of patients with keratoconus (KC), finding that the expression of certain proteins in tears of KC patients differed from the control group. These differences were linked to processes such as cell death, oxidative damage, and inflammation.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Review
Multidisciplinary Sciences
Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin, Neil L. Kelleher
Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.
Article
Microbiology
Charlotte Mappa, Beatrice Alpha-Bazin, Olivier Pible, Jean Armengaud
Summary: Shotgun proteomics is a promising alternative technique for identifying pathogens and characterizing their antimicrobial resistance genes. Proteotyping microorganisms through tandem mass spectrometry is expected to be essential in modern healthcare, and it also plays a crucial role in developing new biotechnological applications through culturomics. Phylopeptidomics is a new strategy that improves the quantification of microbial contributions by estimating phylogenetic distances and calculating the ratio of shared peptides. The study established the limit of detection for tandem mass spectrometry proteotyping and demonstrated the independence of bacterial identification by phylopeptidomics from their growth stage and the robustness of the method in the presence of additional bacteria.
Article
Biochemistry & Molecular Biology
Anna A. Kliuchnikova, Svetlana E. Novikova, Ekaterina V. Ilgisonis, Olga I. Kiseleva, Ekaterina V. Poverennaya, Victor G. Zgoda, Sergei A. Moshkovskii, Vladimir V. Poroikov, Andrey V. Lisitsa, Alexander I. Archakov, Elena A. Ponomarenko
Summary: A meta-analysis was conducted to create a reference standard kit for health analytics by conducting targeted quantitative screening of human blood plasma. The kit includes 53 proteins that are stably present in the proteome of a healthy individual and found in at least 70% of samples, with an interindividual coefficient of variation <40%. These proteins, with concentration range of 10(-10)-10(-3) M, were associated with rare familial diseases based on enrichment analysis. The study also identified specific protein concentration changes in patients with neurological disorders and lung adenocarcinoma compared to healthy volunteers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Multidisciplinary
Xianlin Han, Hongping Ye
Summary: Although triglycerides play important roles in cellular growth, metabolism, and function, accurately identifying their molecular species and quantities remains a challenge.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Food Science & Technology
Bruna Cavecci-Mendonca, Karen Monique Luciano, Tauane Vaccas, Laudiceia Alves de Oliveira, Eloisa Fornaro Clemente, Bruno Cesar Rossini, Jose Cavalcante Souza Vieira, Luciana Curtolo de Barros, Ilka Biondi, Pedro de Magalhaes Padilha, Lucilene Delazari dos Santos
Summary: Snakebite envenoming, a neglected tropical disease, has been studied to understand the protein and metallic ion composition of Brazilian snake venoms. The findings provide insights for potential diagnostic device development.
Article
Biochemistry & Molecular Biology
Zixuan Xie, Chaysavanh Manichanh
Summary: This article introduces a pipeline called FunOMIC, which has built-in taxonomic and functional databases for the identification of fungi. By applying this tool to over 2,600 human metagenomic samples, fungal species associated with geography, body sites, and diseases can be identified, and new insights into inter-kingdom interactions are provided through correlation network analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Analytical
Fei Wang, Jaanus Liigand, Siyang Tian, David Arndt, Russell Greiner, David S. Wishart
Summary: Mass spectrometry (MS) is commonly used in metabolomics for identifying and annotating metabolites. CFM-ID is a computer program that accurately predicts EST-MS/MS spectrum for a given compound structure, improving compound-to-mass-spectrum prediction and in silico mass-spectrum-to-compound identification. This new version of CFM-ID (version 4.0) demonstrates significantly increased accuracy in both ET-MS/MS spectral prediction and compound identification.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Sergio Ciordia, Gloria Alvarez-Sola, Maria Rullan, Jesus M. Urman, Matias A. Avila, Fernando J. Corrales
Summary: The analysis of biological fluids for disease-related proteins is an important field of research. However, challenges exist, especially in complex matrices like bile. A new procedure described in this study significantly improves protein recovery from rat bile, providing valuable resources for further understanding disease molecular markers.
JOURNAL OF PROTEOMICS
(2021)
Article
Microbiology
Alberto Gil-de-la-Fuente, Maricruz Mamani-Huanca, Maria C. Stroe, Sergio Saugar, Alejandra Garcia-Alvarez, Axel A. Brakhage, Coral Barbas, Abraham Otero
Summary: The Aspergillus Metabolome Database is a free online resource with information on 2811 compounds from 601 different species. Users can perform metabolite annotation through m/z searches and access the database through web applications or RESTful services.