Article
Biochemical Research Methods
David J. Degnan, Kelly G. Stratton, Rachel Richardson, Daniel Claborne, Evan A. Martin, Nathan A. Johnson, Damon Leach, Bobbie-Jo M. Webb-Robertson, Lisa M. Bramer
Summary: The pmartR package is designed for QC and analysis of mass spectrometry data, specifically for proteomic, metabolomic, and lipidomic datasets. It has been expanded to include nuclear magnetic resonance metabolomic data and transcriptomic data analysis using DESeq2, edgeR, and limma-voom R packages. The package also offers improved statistics and visualization capabilities, including support for paired data and integration with the trelliscopejs R package.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Chemistry, Analytical
Zengyu Wang, Baohong Liu, Ling Lin, Liang Qiao
Summary: Mitochondria are highly dynamic organelles involved in various cellular processes. Dysfunction of mitochondria is associated with multiple disorders, including neurodegenerative diseases, cardiovascular pathology, aging, and cancer. Significant advancements have been made in mitochondrial biology through the combination of high-throughput omics technologies and biochemical separation techniques. This review focuses on mass spectrometry-based mitochondrial proteomics, metabolomics, and multi-omics integration, as well as the development of machine learning tools for comprehensive and unprecedented insight into mitochondrial uncharted territory.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
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
Computer Science, Theory & Methods
Fahad Saeed, Muhammad Haseeb, S. S. Iyengar
Summary: This paper demonstrates the communication bounds reached by existing parallel proteomics algorithms and argues for the need for next-generation parallel algorithms for MS based large systems biology studies.
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING
(2022)
Article
Biochemistry & Molecular Biology
Emiley A. Eloe-Fadrosh, Faiza Ahmed, Anubhav, Michal Babinski, Jeffrey Baumes, Mark Borkum, Lisa Bramer, Shane Canon, Danielle S. Christianson, Yuri E. Corilo, Karen W. Davenport, Brandon Davis, Meghan Drake, William D. Duncan, Mark C. Flynn, David Hays, Bin Hu, Marcel Huntemann, Julia Kelliher, Sofya Lebedeva, Po-E Li, Mary Lipton, Chien-Chi Lo, Stanton Martin, David Millard, Kayd Miller, Mark A. Miller, Paul Piehowski, Elais Player Jackson, Samuel Purvine, T. B. K. Reddy, Rachel Richardson, Marisa Rudolph, Setareh Sarrafan, Migun Shakya, Montana Smith, Kelly Stratton, Jagadish Chandrabose Sundaramurthi, Pajau Vangay, Donald Winston, Elisha M. Wood-Charlson, Yan Xu, Patrick S. G. Chain, Lee Ann McCue, Douglas Mans, Christopher J. Mungall, Nigel J. Mouncey, Kjiersten Fagnan
Summary: The NMDC Data Portal facilitates exploration and access to multi-omics microbiome data, hosting 10.2 TB of data. The portal utilizes a flexible data schema and workflows to generate annotated data products, offering various interactive search features.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Immunology
Rokhaya Ba, Estelle Geffard, Venceslas Douillard, Francoise Simon, Laurent Mesnard, Nicolas Vince, Pierre-Antoine Gourraud, Sophie Limou
Summary: In the era of big data, the quantity of available data in both research and care is increasing, which presents challenges for patients, caregivers, and researchers. In the field of transplantation, omics studies have greatly impacted research and the understanding of transplant outcomes. Integrating omics data is challenging due to biases and errors, and normalization and imputation methods have been developed to address these issues. The transplantation field brings additional complexity to omics analysis, and new strategies such as combined risk scores are emerging to better understand graft mechanisms.
Article
Biochemical Research Methods
Edouard C. Nice
Summary: The field of proteomics has made significant progress in the past decade, with the development of a comprehensive toolbox and the integration of proteomics with other omics platforms. These advancements have provided important insights into the molecular changes leading to diseases and have the potential to identify biomarkers and drug targets. The translation of discovery-based findings to clinical applications has also supported the implementation of precision/personalized medicine. However, challenges in Big Data analysis still need to be addressed.
ANALYTICAL BIOCHEMISTRY
(2022)
Article
Biochemical Research Methods
Carolyn Allen, Rico Meinl, J. Sebastian Paez, Brian C. Searle, Seth Just, Lindsay K. Pino, William E. Fondrie
Summary: This study presents an open-source NextFlow pipeline, nf-encyclopedia, which connects three open-source tools (MSConvert, EncyclopeDIA, and MSstats) for analyzing DIA proteomics experiments with or without chromatogram libraries. The pipeline is reproducible and provides robust peptide and protein quantification. MSstats improves protein-level quantification performance over EncyclopeDIA alone.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Chemistry, Analytical
Hanne Roberg-Larsen, Elsa Lundanes, Tuula A. Nyman, Frode S. Berven, Steven Ray Wilson
Summary: Single-cell analysis provides in-depth insights into diseases and diagnostics, with liquid chromatography playing a crucial role. The development of novel sample preparation techniques and improvements in mass spectrometry are enhancing the promise of single-cell analysis. However, technical challenges and the need for higher throughput and robustness may lead to the reinvention of alternative nano LC column formats.
ANALYTICA CHIMICA ACTA
(2021)
Article
Biochemistry & Molecular Biology
Yewei Wang, Zeljka Popovic, Georgia Charkoftaki, Rolando Garcia-Milian, TuKiet T. Lam, David C. Thompson, Ying Chen, Vasilis Vasiliou
Summary: This study identifies the impact of knocking down ALDH1B1 on molecular signatures in colon cancer cells through multi-omics analysis. The findings provide new molecular information associated with the cellular functions of ALDH1B1, which will guide future investigations of colon cancer.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Chemistry, Applied
Rong Zhang, Wei Jia, Meng Zhang, Haiyan Xue, Huxuan Wang, Xixuan Wu
Summary: The influence of magnetic field treatment on glycation of goat milk proteins is not yet fully understood. Proteomic and metabolomic analyses revealed that magnetic field treatment significantly reduced glycation of brown goat milk proteins, possibly due to induced aggregation behavior that consumed additional glycation sites and altered their accessibility and preference. Integrated datasets suggested that energy metabolism-related biological events may be the main mechanism behind the reduction in browning with magnetic field treatment. Additionally, magnetic field treatment improved the quality and flavor of brown goat milk. This study highlights the feasibility of using magnetic field treatment to reduce glycation in brown goat milk for producing high-quality dairy ingredients and products.
Review
Spectroscopy
Leena R. Pade, Kaitlyn E. Stepler, Erika P. Portero, Kellen DeLaney, Peter Nemes
Summary: Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Mass spectrometry (MS) has advanced significantly, allowing for precise analysis of molecular architecture at various levels, with high detection sensitivity and scalability. This review highlights technology innovations that have improved sample collection and processing, chemical separation, ionization, and 'omics analyses, enabling deeper study of limited and dynamic specimens. The integration of orthogonal approaches from molecular and functional studies, combined with spatiotemporal MS, has become an exciting and powerful resource in the study of biological systems.
MASS SPECTROMETRY REVIEWS
(2023)
Review
Biochemical Research Methods
Haiyan Lu, Hua Zhang, Lingjun Li
Summary: Single-cell analysis provides new insights into the study of fundamental biological phenomena and cellular heterogeneity. Mass spectrometry has emerged as a leading technology for molecular profiling of single-cell omics, but it faces challenges such as ionization suppression and low concentration. Chemical tagging/derivatization has proven to be an effective solution to overcome these challenges in single-cell mass spectrometry analysis.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Aleesa E. Chua, Leah D. Pfeifer, Emily R. Sekera, Amanda B. Hummon, Heather Desaire
Summary: To achieve high quality omics results, addressing systematic variability in mass spectrometry data through effective data normalization is essential. While there are open-source academic software available for selecting the best approach, they may not meet the needs of all users. In this study, a simple workflow using intuitive evaluation metrics and machine learning is proposed to identify the optimal normalization strategies, which can be applied to any type of MS data.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Matt Spick, Amy Campbell, Ivona Baricevic-Jones, Johanna von Gerichten, Holly-May Lewis, Cecile F. Frampas, Katie Longman, Alexander Stewart, Deborah Dunn-Walters, Debra J. Skene, Nophar Geifman, Anthony D. Whetton, Melanie J. Bailey
Summary: Treatments for COVID-19 infections have improved, with glucocorticoids playing a key role in reducing mortality rates. However, a study has found that glucocorticoids are not fully effective in addressing the diverse range of 'omics dysregulation caused by COVID-19 infections.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
