Article
Biochemical Research Methods
Andrew R. Jones, Eric W. Deutsch, Juan Antonio Vizcaino
Summary: DIA proteomics techniques have made significant progress in recent years, but there is still room for improvement in terms of FAIR data principles. To enhance the current situation for DIA data, recommendations include developing an open data standard for spectral libraries, mandating the availability of spectral libraries in ProteomeXchange resources, improving support for DIA data in data standards, and enhancing support for DIA datasets in ProteomeXchange resources.
Article
Food Science & Technology
Lana S. Rosa, Mariana L. Santos, Joel P. Abreu, Ramon S. Rocha, Erick A. Esmerino, Monica Q. Freitas, Eliane T. Marsico, Pedro H. Campelo, Tatiana C. Pimentel, Marcia Cristina Silva, Adrieli A. Souza, Fabio C. S. Nogueira, Adriano G. Cruz, Anderson J. Teodoro
Summary: The effect of probiotic strains on fermented whey-milk beverages was evaluated during storage. The addition of probiotics increased α-amylase and α-glucosidase inhibition and antioxidant activities, with the best effect observed after 15 days of storage. L. casei-01 showed higher metabolic activity and the presence of anti-hypertensive peptides, while La-5 and Bb-12 showed improvements in alpha-glucosidase inhibition and the presence of peptides with various activities.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Biochemical Research Methods
Ananth Prakash, David Garcia-Seisdedos, Shengbo Wang, Deepti Jaiswal Kundu, Andrew Collins, Nancy George, Pablo Moreno, Irene Papatheodorou, Andrew R. Jones, Juan Antonio Vizcaino
Summary: The availability of proteomics datasets, especially in the PRIDE database, has significantly increased in recent years, providing an opportunity for combined analyses of datasets to obtain organism-wide protein abundance data. In this study, we reanalyzed 24 public proteomics datasets to assess baseline protein abundance in 31 organs of healthy individuals. We compared protein abundances between organs, studied protein distribution, and performed gene ontology and pathway-enrichment analyses. The results are integrated into the Expression Atlas resource to enhance accessibility for life scientists.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Eric W. Deutsch, Juan Antonio Vizcaino, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, Yasset Perez-Riverol, David L. Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D. Mak, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C. E. Tosatto, Sandra E. Orchard
Summary: The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been developing guidelines and standards for the proteomics community for 20 years. The organization describes its operation, the current state of existing standards, and the proposals currently being developed. They emphasize the importance of community participation and collaboration with other organizations to promote data sharing and accelerate progress in proteomics.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwaemmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
David L. Tabb, Kyowon Jeong, Karen Druart, Megan S. Gant, Kyle A. Brown, Carrie Nicora, Mowei Zhou, Sneha Couvillion, Ernesto Nakayasu, Janet E. Williams, Haley K. Peterson, Michelle K. McGuire, Mark A. McGuire, Thomas O. Metz, Julia Chamot-Rooke
Summary: This study evaluates four top algorithms for top-down identification in their yield of PrSMs while controlling false discovery rate. The study finds that these algorithms perform well in generating PrSMs, but approximately half of the identified proteoforms are specific to only one algorithm. Deconvolution algorithms show inconsistency in precursor charges and mass determinations, contributing to identification variability. Detection of post-translational modifications is also inconsistent among algorithms. Applying multiple search engines provides more comprehensive assessments of experiments, and there is a need for greater interoperability of top-down algorithms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Virology
Marlonni Maurastoni, Tathiana Sa F. Antunes, Emanuel F. M. Abreu, Simone G. Ribeiro, Angela Mehta, Marcio M. Sanches, Wagner Fontes, Elliot W. Kitajima, Fabiano T. Cruz, Alexandre M. C. Santos, Jose A. Ventura, Ana C. M. M. Gomes, F. Murilo Zerbini, Patricia Sosa-Acosta, Fabio C. S. Nogueira, Silas P. Rodrigues, Francisco J. L. Aragao, Anna E. Whitfield, Patricia M. B. Fernandes
Summary: Papaya sticky disease is caused by papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2). Two major proteins were identified in the purified virus. A potential interaction between the viral proteins and the 50S ribosomal protein L17 (AtRPL17) was discovered, suggesting the importance of virus-host interactions in the disease.
Article
Biochemical Research Methods
Matthys J. Potgieter, Andrew J. M. M. Nel, Suereta Fortuin, Shaun Garnett, Jerome Wendoh, David Tabb, Nicola Mulder, Jonathan Blackburn
Summary: MetaNovo is an open-source software pipeline that integrates existing tools with a custom algorithm to produce targeted protein sequence databases for mass spectrometry metaproteomic analysis as an intermediate filtering step prior to standard sequence database search approaches. The software uses open-source tools to match peptide mass spectrometry spectra to sequence database entries and can be installed in a cluster or run standalone on a Linux machine. It is relevant for analyzing protein data from multiple organisms, where the exact species composition is unknown, and provides an avenue for analysis when accurate taxonomic characterization is not available.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Mathias Walzer, Kyowon Jeong, David L. Tabb, Juan Antonio Vizcaino
Summary: Although Top-down (TD) proteomics techniques are gaining popularity in intact protein and proteoform analysis, efforts are required to promote their adoption at different levels. Open science practices, including data sharing and open data analysis workflows, need to be improved and implemented.
Article
Microbiology
Pamela Donoso-Pinol, Gabriela Briceno, Joseph A. M. Evaristo, Fabio C. S. Nogueira, Barbara Leiva, Claudio Lamilla, Heidi Schalchli, Maria Cristina Diez
Summary: Iprodione, a highly toxic compound, is still used in many places around the world despite restrictions, posing an environmental risk. This study isolated thirteen IPR-tolerant bacteria from a pesticide treatment system and found that Achromobacter sp. C1 had the highest degradation rate. Proteomic analysis revealed proteins related to IPR treatment, particularly amidases.
Article
Biotechnology & Applied Microbiology
Tammy Boggiano-Ayo, Julio Palacios-Oliva, Sumlai Lozada-Chang, Ernesto Relova-Hernandez, Jose Gomez-Perez, Gonzalo Oliva, Lourdes Hernandez, Alexi Bueno-Soler, Daidee Montes de Oca, Osvaldo Mora, Roberto Machado-Santisteban, Dayana Perez-Martinez, Beatriz Perez-Masson, Yanelys Cabrera Infante, Lisandra Calzadilla-Rosado, Yaima Ramirez, Judey Aymed-Garcia, Ingrid Ruiz-Ramirez, Yamile Romero, Tania Gomez, Luis A. Espinosa, Luis Javier Gonzalez, Annia Cabrales, Osmany Guirola, Kathya Rashida de la Luz, Franciscary Pi-Estopinan, Belinda Sanchez-Ramirez, Dagmar Garcia-Rivera, Yuri Valdes-Balbin, Gertrudis Rojas, Kalet Leon-Monzon, Eduardo Ojito-Magaz, Eugenio Hardy
Summary: We have developed a single process for producing two key COVID-19 vaccine antigens - SARS-CoV-2 receptor binding domain (RBD) monomer and dimer. Our approach involves expressing RBD in CHO-K1 cells, selecting the best RBD-producing clones, and purifying the antigens using various chromatography techniques. The unified manufacturing process provides the necessary flexibility to adapt to emerging SARS-CoV-2 variants and different COVID-19 vaccine platforms.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Nancy George, Silvie Fexova, Alfonso Munoz Fuentes, Pedro Madrigal, Yalan Bi, Haider Iqbal, Upendra Kumbham, Nadja Francesca Nolte, Lingyun Zhao, Anil S. Thanki, Iris D. Yu, Jose C. Marugan Calles, Karoly Erdos, Liora Vilmovsky, Sandeep R. Kurri, Anna Vathrakokoili-Pournara, David Osumi-Sutherland, Ananth Prakash, Shengbo Wang, Marcela K. Tello-Ruiz, Sunita Kumari, Doreen Ware, Damien Goutte-Gattat, Yanhui Hu, Nick Brown, Norbert Perrimon, Juan Antonio Vizcaino, Tony Burdett, Sarah Teichmann, Alvis Brazma, Irene Papatheodorou
Summary: Expression Atlas and Single Cell Expression Atlas are knowledgebases for gene and protein expression and localisation, covering bulk and single cell levels of data respectively. Users can search genes or metadata across species and explore data through dimensionality reduction plots and heatmaps to understand the expression patterns.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Panni Simona, Kalpana Panneerselvam, Pablo Porras, Margaret Duesbury, Livia Perfetto, Luana Licata, Henning Hermjakob, Sandra Orchard
Summary: In this paper, the authors present a method of annotating microRNA-mRNA interactions from the scientific literature. They focus on microRNAs that regulate genes associated with rare diseases and provide a detailed description of cell types and experimental conditions to enhance the information about the interactions. The authors also highlight the importance of mapping the binding sites of microRNAs on target genes' mRNA transcripts.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)