Article
Biochemical Research Methods
Andrea Fossati, Chen Li, Federico Uliana, Fabian Wendt, Fabian Frommelt, Peter Sykacek, Moritz Heusel, Mahmoud Hallal, Isabell Bludau, Tumay Capraz, Peng Xue, Jiangning Song, Bernd Wollscheid, Anthony W. Purcell, Matthias Gstaiger, Ruedi Aebersold
Summary: The study introduces a toolkit called PCprophet that predicts protein complexes and characterizes their changes using SEC-SWATH-MS data. PCprophet demonstrates improved performance compared to other methods and introduces a Bayesian approach to analyze changes in protein-protein interactions.
Article
Biochemical Research Methods
Mark Ivanov, Elizaveta M. Solovyeva, Julia A. Bubis, Mikhail Gorshkov
Summary: Protein inference is a crucial step in proteome characterization using a bottom-up approach, and this study proposes a method using peptide feature information from precursor mass spectra to assist in distinguishing homologous proteins more accurately and efficiently.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Eric W. Deutsch, Luis Mendoza, David D. Shteynberg, Michael R. Hoopmann, Zhi Sun, Jimmy K. Eng, Robert L. Moritz
Summary: The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has undergone continuous development and refinement since the publication of its first tools, PeptideProphet and ProteinProphet, 20 years ago. The latest release offers a wide range of tools for spectrum processing, spectrum searching, search validation, abundance computation, protein inference, and more. These tools incorporate machine-learning modeling to maximize information extraction and establish robust statistical models for accurate information derivation. This article presents an overview of the latest TPP tools, their deployment on different platforms, tutorials for their usage, and synergistic projects leveraging TPP. The article concludes with outlined plans for future TPP development.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Health Care Sciences & Services
Abdul Rafay, Muzzamil Aziz, Amjad Zia, Abdul R. R. Asif
Summary: Proteomics instrumentation and bioinformatics tools have advanced rapidly in the past 20 years, and there is potential for using deep learning techniques in proteomics. This study proposes a workflow to create a linked dataset of heart-related proteomic data, which can be used for machine learning and deep learning algorithms to predict and model heart diseases in the future.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Review
Biochemistry & Molecular Biology
Xiying Chen, Zhouyuanjing Shi, Feng Yang, Tianhua Zhou, Shanshan Xie
Summary: Cilia are microtubule-based organelles that play crucial roles in cellular signaling pathways and extracellular fluid movement. Defects in ciliary structures and functions are implicated in hereditary disorders known as ciliopathies. Proteomic studies provide important clues for understanding the physiological and pathological roles of cilia.
Article
Biochemical Research Methods
Oliver Kardell, Stephan Breimann, Stefanie M. Hauck
Summary: mpwR is an R package designed for standardized comparison of mass spectrometry-based proteomic label-free workflows. It allows easy access to compare the impact of sample preparation procedures, combinations of liquid chromatography-MS setups, and software differences on critical performance measures across multiple analyses. mpwR supports outputs of commonly used software for bottom-up proteomics like ProteomeDiscoverer, Spectronaut, MaxQuant, and DIA-NN.
Article
Biochemistry & Molecular Biology
Wendell Albuquerque, Parviz Ghezellou, Leif Seidel, Johannes Burkert, Frank Will, Ralf Schweiggert, Bernhard Spengler, Holger Zorn, Martin Gand
Summary: This study presents the first comprehensive identification of proteome content from a white wine (cv. Silvaner). By using mass spectrometry-based proteomics, the wine protein composition was identified through in-solution and in-gel digestion methods after size exclusion chromatographic fractionation. A total of 154 characterized or uncharacterized proteins mainly from Vitis vinifera L. and Saccharomyces cerevisiae were identified, providing valuable information for wine authentication and understanding of organoleptic properties and stability.
Article
Biochemistry & Molecular Biology
Ruta Navakauskiene, Sandra Baronaite, Dalius Matuzevicius, Natalija Krasovskaja, Grazina Treigyte, Audrone Arlauskiene, Dalius Navakauskas
Summary: Mass spectrometry-based proteomics was used to analyze amniotic fluid samples and identify proteins related to normal and polyhydramnios pregnancies. Quantitative changes in proteins were evaluated through computational analysis and comparison of protein maps. The study found that certain proteins showed increased levels in pathological pregnancies, suggesting their association with immune response, inflammation, and abnormal development. This research provides insights into the mechanisms underlying pathological pregnancies and fetal abnormalities.
Article
Medical Laboratory Technology
Ximeng Chen, Jianan Wang, Jinyang Wang, Jingyun Ye, Ping Di, Chang Dong, Hong Lei, Chengbin Wang
Summary: This study utilized proteomics to analyze serum proteins and identify potential biomarkers for the diagnosis of osteoarticular tuberculosis. ITIH2, CFHR2, CFHR3, and CFHR5 were found to be potential biomarkers, with CFHR2 and CFHR3 showing good diagnostic efficacy when combined in a diagnostic model.
CLINICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Maria Isabel Alcoriza-Balaguer, Juan Carlos Garcia-Canaveras, Francisco Javier Ripoll-Esteve, Marta Roca, Agustin Lahoz
Summary: In this study, LipidMS 3.0, an R package, was introduced for the whole data analysis workflow from pre-processing to lipid annotation. Compared to existing tools, LipidMS 3.0 performs similarly in data pre-processing performance but provides a higher level of structural information and fewer incorrect annotations in lipid annotation.
Article
Biochemical Research Methods
Mark P. Molloy, Cameron Hill, Matthew B. O'Rourke, Jason Chandra, Pascal Steffen, Matthew J. McKay, Dana Pascovici, Ben R. Herbert
Summary: Microsampling of patient blood using the volumetric absorptive microsampling (VAMS) device enables LC-MS proteomic analyses of dried whole blood and enhances the proteome depth compared to conventional plasma analysis. This method also allows preferential removal of proteins and is compatible with long-term stored frozen blood cell pellets. These findings are important for establishing analysis workflows in large-scale precision medicine studies.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ozgur Yurekten, Thomas Payne, Noemi Tejera, Felix Xavier Amaladoss, Callum Martin, Mark Williams, Claire O'Donovan
Summary: MetaboLights is a global database for metabolomics studies that contains raw experimental data and associated metadata. It includes metabolite structures, reference spectra, and biological roles. This article discusses the growth and diversity of submissions to the database and highlights the development of MetaboLights Labs, a standardized workflow platform. The reuse of data by the community is also emphasized.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Ekaterina Mikhailovna Stakhneva, Evgeniia Vitalievna Striukova, Yulia Igorevna Ragino
Summary: Proteomic studies play a crucial role in investigating atherosclerotic cardiovascular diseases, identifying potential biomarkers, and offering novel diagnostic approaches.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Congcong Lu, Tina Glisovic-Aplenc, Kathrin M. Bernt, Kevin Nestler, Joseph Cesare, Lusha Cao, Hyoungjoo Lee, Hossein Fazelinia, Asif Chinwalla, Yang Xu, Olga Shestova, Yi Xing, Saar Gill, Mingyao Li, Benjamin Garcia, Richard Aplenc
Summary: This study evaluated the performance of three LC-MS platforms in label-free semiquantitative analysis of cell surface proteins over a six-year period, showing consistent detection and reproducible quantification of a large number of cell surface proteins across all three platforms using the established workflow. This is the first study to report highly reproducible semiquantitative proteomic data collection of biological replicates across multiple years and LC-MS platforms.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Laura Darie-Ion, Madhuri Jayathirtha, Gabriela Elena Hitruc, Marius-Mihai Zaharia, Robert Vasile Gradinaru, Costel C. Darie, Aurel Pui, Brindusa Alina Petre
Summary: Through combining different analytical methods, zein protein was extracted including mass spectrometry, SDS-PAGE, AFM, and FTIR-ATR. The use of ultrasonic extraction method with 65% ethanol extraction buffer and 710 mu m maize granulation yielded the highest protein extraction. The extracted zein was mainly alpha-zein monomer according to SDS-PAGE analysis and the main component in maize flour extract was alpha-zein PMS2 protein based on MS analysis. A homogeneous content of extracted zein could potentially be used for future medical applications according to AFM studies.