Article
Plant Sciences
Lara Garcia-Campa, Luis Valledor, Jesus Pascual
Summary: To improve the quality of reference databases and their annotations, researchers combined full-length isoform sequencing (Iso-Seq) with short-read transcriptomics and proteomics. By including Oxford Nanopore Technologies Direct RNA Sequencing (ONT-DRS) data, they enhanced the identification and discovery of proteoforms in Arabidopsis MS proteomics data. This approach offers unprecedented opportunities for investigating biological systems, but also presents challenges for existing protein searching algorithms.
Article
Biochemical Research Methods
Noe Guilloy, Marie A. Brunet, Sebastien Leblanc, Jean-Francois Jacques, Marie-Pierre Hardy, Gregory Ehx, Joel Lanoix, Pierre Thibault, Claude Perreault, Xavier Roucou
Summary: Proteomic diversity in biological samples can be characterized using mass spectrometry (MS)-based proteomics and customized protein databases generated from RNA-seq data. The recent discovery of translated alternative open reading frames in mRNAs and ncRNAs has increased this diversity. To fill the gap in current computational workflows, OpenCustomDB is a bioinformatics tool that identifies genomic variants in both canonical and alternative open reading frames using sample-specific RNA-seq data. It has been shown to detect a significant number of peptides from alternative proteins in a cohort of acute myeloid leukemia patients.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Analytical
Nicole E. Avalon, Alison E. Murray, Bill J. Baker
Summary: The pairing of analytical chemistry with genomic techniques has brought a new wave of research in natural product chemistry. This combination allows for the exploration of the biosynthetic capabilities of microorganisms with valuable secondary metabolites. However, the development of efficient and accessible tools is vital to overcome the challenges in connecting metabolic potential and compound isolation. Innovative approaches have been proven useful in early stages of microbial genome-informed drug discovery, leading to better prioritization of targets and reduced rediscovery rates. Comparative evolutionary studies and retrobiosynthetic predictions have also contributed to understanding biosynthetic mechanisms and linking genome sequences to chemical structures. Advancements in engineering, chemistry, and computational technologies have accelerated progress in omic-informed natural product drug discovery. These strategies enhance the synergy between cutting-edge omics, chemical characterization, and computational approaches, propelling the discovery of natural products with pharmaceutical and other potential applications.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Seungjin Na, Hyunjin Choi, Eunok Paek
Summary: In this study, a predicted Spectral DataBase (pSDB) search strategy called Deephos was proposed to improve the identification of TMT-labeled phosphopeptides in MS/MS spectra. By utilizing deep learning-based fragment ion prediction, a pSDB of TMT-labeled phosphopeptides was compiled. The study also discussed the generation of decoy spectra for more accurate estimation of false discovery rate (FDR). The utilities of Deephos were demonstrated in the analysis of three cancer phosphoproteomes.
Article
Multidisciplinary Sciences
Tim Van den Bossche, Benoit J. Kunath, Kay Schallert, Stephanie S. Schaepe, Paul E. Abraham, Jean Armengaud, Magnus O. Arntzen, Ariane Bassignani, Dirk Benndorf, Stephan Fuchs, Richard J. Giannone, Timothy J. Griffin, Live H. Hagen, Rashi Halder, Celine Henry, Robert L. Hettich, Robert Heyer, Pratik Jagtap, Nico Jehmlich, Marlene Jensen, Catherine Juste, Manuel Kleiner, Olivier Langella, Theresa Lehmann, Emma Leith, Patrick May, Bart Mesuere, Guylaine Miotello, Samantha L. Peters, Olivier Pible, Pedro T. Queiros, Udo Reichl, Bernhard Y. Renard, Henning Schiebenhoefer, Alexander Sczyrba, Alessandro Tanca, Kathrin Trappe, Jean-Pierre Trezzi, Sergio Uzzau, Pieter Verschaffelt, Martin von Bergen, Paul Wilmes, Maximilian Wolf, Lennart Martens, Thilo Muth
Summary: The CAMPI project is a large-scale multi-lab comparison of metaproteomics workflows. The study shows that variability at the peptide level is mainly due to sample processing workflows, with a smaller contribution from bioinformatic pipelines. While differences are observed in predicted community composition, similar functional profiles are obtained across workflows.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Wai-Kok Choong, Ting-Yi Sung
Summary: In protein-based variant sequence databases, the reverse or pseudo reverse method yields similar performance for variant peptide identification, while in the peptide-based databases, the pseudo reverse method is more suitable than the widely used reverse method for identifying more variant PSMs.
JOURNAL OF PROTEOMICS
(2021)
Article
Biotechnology & Applied Microbiology
Martin A. Hoffmann, Louis-Felix Nothias, Marcus Ludwig, Markus Fleischauer, Emily C. Gentry, Michael Witting, Pieter C. Dorrestein, Kai Duehrkop, Sebastian Boecker
Summary: The COSMIC workflow combines in silico structure database generation and annotation with a confidence score for accurate and efficient metabolite annotation. It outperforms spectral library search by annotating a substantial number of hits at low false discovery rates and can successfully annotate structures never reported before.
NATURE BIOTECHNOLOGY
(2022)
Article
Chemistry, Applied
Wenlin Wu, Shiyao Liu, Tianrong Guo, Xiying Han, Bing Xia, Yuping Wan, Quanbin Han, Yan Zhou
Summary: A rapid screening method for 70 colorants in dyeable foods was established using UHPLC-Q/Orbitrap MS with customized accurate-mass database and mass spectral library. The method utilized ultrasound-assisted extraction and dispersion solid-phase extraction for sample pretreatment, and evaluated performance in terms of various parameters. The method showed great potential for broad, sensitive, and reliable analysis of colorants in different foods.
Review
Biochemical Research Methods
Andrew T. Rajczewski, Pratik D. Jagtap, Timothy J. Griffin
Summary: Proteomics, using mass spectrometry, is a valuable tool in biomedical and basic biological research to identify proteins in a system of interest. When integrated with other 'omics' data, such as transcriptomics, genomics, and metabolomics, it provides a more comprehensive understanding of biological systems and their responses to stimuli. This integration, known as multi-omics, requires complete and accurate proteomics data and can be challenging for inexperienced researchers.
EXPERT REVIEW OF PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Alexander E. Ostrovsky, Alexandru Mahmoud, Andrew J. Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anton Nekrutenko, Anup Kumar, Arthur C. Eschenlauer, Assunta D. DeSanto, Aysam Guerler, Beatriz Serrano-Solano, Berenice Batut, Bjoern A. Gruening, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristobal Gallardo, Daniel Blankenberg, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Lariviere, Engy Nasr, Enis Afgan, Federico Zambelli, Florian Heyl, Fotis Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguille, Greg Von Kuster, Gulsum Gudukbay Akbulut, Helena Rasche, Hotz Hans-Rudolf, Ignacio Eguinoa, Igor Makunin, Isuru J. Ranawaka, James P. Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, Jeremy Goecks, John M. Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Le Bras Yvan, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie C. Foell, Michael C. Schatz, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan A. Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Vandenbrouck Yves, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem de Koning, Wolfgang Maier, Peter J. Briggs
Summary: Galaxy is a mature and browser accessible workbench for scientific computing, allowing scientists to easily share, analyze, and visualize their data. It has a strong global community and support from national infrastructure providers. Key technical developments of Galaxy include improved user interface, interactive tools for data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Adam L. Edwinson, Lu Yang, Stephanie Peters, Nikita Hanning, Patricio Jeraldo, Pratik Jagtap, Joshua B. Simpson, Tzu-Yi Yang, Praveen Kumar, Subina Mehta, Asha Nair, Margaret Breen-Lyles, Lakshmikanth Chikkamenahalli, Rondell P. Graham, Benedicte De Winter, Robin Patel, Surendra Dasari, Purna Kashyap, Timothy Griffin, Jun Chen, Gianrico Farrugia, Matthew R. Redinbo, Madhusudan Grover
Summary: Intestinal protease activity is suppressed by gut microbiota through the production of unconjugated bilirubin. In irritable bowel syndrome patients, an altered gut microbiota composition results in increased protease activity.
NATURE MICROBIOLOGY
(2022)
Article
Virology
Subina Mehta, Valdemir M. Carvalho, Andrew T. Rajczewski, Olivier Pible, Bjoern A. Gruening, James E. Johnson, Reid Wagner, Jean Armengaud, Timothy J. Griffin, Pratik D. Jagtap
Summary: The COVID-19 pandemic caused by the SARS-CoV-2 virus has resulted in a global health crisis, with the emergence of new strains posing challenges in detection. Mass spectrometry (MS)-based methods can help in diagnosing and developing vaccines by detecting and characterizing variant-specific peptide sequences from viral proteins. In this study, a bioinformatics workflow was developed to detect variant-specific peptide sequences from MS data derived from clinical samples. The workflow was shown to be effective in characterizing clinical data from different parts of the world, identifying six SARS-CoV-2 variant-specific peptides suitable for confident detection by MS in commonly collected clinical samples.
Article
Respiratory System
Sarah Samorodnitsky, Eric F. Lock, Monica Kruk, Alison Morris, Janice M. Leung, Ken M. Kunisaki, Timothy J. Griffin, Chris H. Wendt
Summary: This study used aptamer proteomics to identify proteins and associated pathways in HIV-associated obstructive lung disease. The results showed that protein expression differs in persons living with HIV with and without obstructive lung disease. A unique protein endotype associated with insulin and apoptotic pathways was identified.
Review
Chemistry, Medicinal
Kevin J. Murray, Peter W. Villalta, Timothy J. Griffin, Silvia Balbo
Summary: The identification of covalently modified biomolecules, secondary metabolites, and xenobiotics is challenging in global metabolomics profiling. Liquid chromatography-coupled mass spectrometry (LC-MS) small molecule analytical workflows have been developed for the detection and characterization of these compounds. Continued advances in these methods expand the capacity for selective compound discovery and characterization.
CHEMICAL RESEARCH IN TOXICOLOGY
(2023)
Review
Biochemical Research Methods
Subina Mehta, Matthias Bernt, Matthew Chambers, Matthias Fahrner, Melanie Christine Foell, Bjoern Gruening, Carlos Horro, James E. Johnson, Valentin Loux, Andrew T. Rajczewski, Oliver Schilling, Yves Vandenbrouck, Ove Johan Ragnar Gustafsson, W. C. Mike Thang, Cameron Hyde, Gareth Price, Pratik D. Jagtap, Timothy J. Griffin
Summary: The Galaxy ecosystem offers a range of open-source tools for MS-based proteomics analyses, providing an adaptable, scalable, and accessible computing environment. This community-supported resource is crucial for basic biological and clinical studies, and ongoing developments are underway to meet emerging challenges in MS-based proteomic informatics.
EXPERT REVIEW OF PROTEOMICS
(2023)
Article
Biochemical Research Methods
Surbhi Bihani, Aryan Gupta, Subina Mehta, Andrew T. Rajczewski, James Johnson, Dhanush Borishetty, Timothy J. Griffin, Sanjeeva Srivastava, Pratik D. Jagtap
Summary: During the COVID-19 pandemic, the exploration of the microbiome is necessary due to impaired immunity and cases of secondary infections. This study used mass spectrometry-based data to investigate the metaproteome of nasopharyngeal swab samples from COVID-19 patients. Through a bioinformatics workflow, microbial peptides belonging to opportunistic pathogens were detected, and upregulated microbial proteins were found in severe patients. Clinical metaproteomics based on mass spectrometry can be a powerful tool for detecting and characterizing potential pathogens, impacting the diagnosis and treatment of patients.
JOURNAL OF PROTEOME RESEARCH
(2023)
Letter
Respiratory System
Li Li, Brian Vestal, Margaret M. Mroz, Sucai Liu, Kristyn MacPhail, Tim J. Griffin, Ivana V. Yang, Lisa A. Maier, Maneesh Bhargava
Article
Biochemistry & Molecular Biology
Andrew T. Rajczewski, Qiyuan Han, Subina Mehta, Praveen Kumar, Pratik D. Jagtap, Charles G. Knutson, James G. Fox, Natalia Y. Tretyakova, Timothy J. Griffin
Summary: Chronic inflammation of the colon can lead to the expression of non-canonical protein sequences, contributing to oncogenesis. This study used a mouse model to induce chronic inflammation and generated a customized database of non-canonical protein sequences. Through proteogenomic analysis, several non-canonical peptide sequences were identified and validated. The study highlights the challenges of identifying non-canonical peptides and provides an integrated workflow to address these challenges.