Related references
Note: Only part of the references are listed.
Article
Biochemical Research Methods
Ananth Prakash et al.
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
Andrew R. Jones et al.
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
Biochemistry & Molecular Biology
Brian T. Lee et al.
Summary: The UCSC Genome Browser is a graphical viewer for exploring genome annotations, providing integrated tools for visualizing, comparing, analyzing, and sharing genomic datasets. Updates this year include new public hub assemblies for new organisms, updated clinical tracks, a new Track Sets feature, enhanced variant displays, and a tool for placing new SARS-CoV-2 genomes in a global phylogenetic tree. Other improvements focus on usability features such as informative mouseover displays and new fonts.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Pablo Moreno et al.
Summary: EMBL-EBI Expression Atlas is a knowledge base that integrates data from over 4500 expression studies across different species, enabling researchers to explore the expression patterns of genes or proteins under various biological conditions. The data are curated by experts, re-analyzed, and visualized in an easily accessible form, aiming to reproduce the original conclusions of the experiments.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ludwig Lautenbacher et al.
Summary: ProteomicsDB is a multi-omics and multi-organism resource for life science research, with efforts to improve the findability, accessibility, interoperability and reusability of data. New API and UI have been released, along with content expansions into different human biology and a newly supported organism.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Toshihisa Okido et al.
Summary: The Bioinformation and DDBJ (DNA Data Bank of Japan) Center operates archival databases and provides services for life science researchers, including nucleotide sequences, study information, and other genomic data-related services.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Yasset Perez-Riverol et al.
Summary: PRIDE is the largest data repository of mass spectrometry-based proteomics data in the world, with around 500 datasets submitted per month. In addition to continuous improvements in data pipelines and infrastructure, PRIDE has developed the Spectra Archive and MAGE-TAB file format to enhance sample metadata annotation and access to mass spectra.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Mallory Ann Freeberg et al.
Summary: The European Genome-phenome Archive (EGA) is a resource for secure archiving of genetic, phenotypic, and clinical data, promoting data reuse, reproducibility, and accelerating biomedical research. EGA operates a distributed data access model, providing strong data protection control.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Tao Chen et al.
Summary: The iProX integrated proteome resource has been greatly improved with an up-to-date big data platform to support large-scale data storage, efficient querying, and reanalysis, meeting the demands of the rapidly growing field of proteomics.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Fiona Cunningham et al.
Summary: Ensembl is unique in its flexible infrastructure for access to genomic data and annotation. They have focused on expediting annotation of new assemblies via the Ensembl Rapid Release platform, with the greatest annual number of newly annotated genomes released. They also developed a new method for comparative analyses and annotated non-vertebrate eukaryotes for the first time.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Richard D. LeDuc et al.
Summary: It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence. The ProForma 2.0 notation aims to unify the representation of proteoforms and peptidoforms, supporting different proteomics approaches and allowing the encoding of highly modified proteins and peptides using a human- and machine-readable string.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Kerry A. Ramsbottom et al.
Summary: Phosphoproteomic methods are used to identify and quantify phosphorylation sites on proteins. This study introduces the concept of scoring modifications on a decoy amino acid to estimate the global false localization rate (FLR) independently.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Multidisciplinary Sciences
Mehar Un Nissa et al.
Summary: Rohu is an important fish species in aquaculture, and integrative omics research provides a platform for understanding its biology. By utilizing mass spectrometry-based proteomics, an open source PeptideAtlas for Rohu has been developed, which has significant implications for aquaculture research and addressing food security challenges.
Article
Multidisciplinary Sciences
Charles Tapley Hoyt et al.
Summary: The standardized identification of biomedical entities is important for interoperability and data integration in the life sciences. The Bioregistry is an integrative and open metaregistry that expands upon existing registries to address the evolving needs of researchers. By leveraging public infrastructure and automation, and employing an open code and open data governance model, the Bioregistry promotes interoperability and reuse of data and scientific literature.
Letter
Biotechnology & Applied Microbiology
Jonathan M. Mudge et al.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Shengbo Wang et al.
Summary: By reanalyzing public proteomics datasets, the baseline protein abundance in mouse and rat tissues was assessed and compared across different organs and species. The findings were integrated into the Expression Atlas resource for dissemination.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Mathias Walzer et al.
Summary: This study introduces a re-analysis pipeline for public SWATH-MS datasets, which includes automated workflows and statistical analysis, and integrates the results into the Expression Atlas resource. By reanalysing 10 public DIA datasets, the robustness of the pipeline was validated, and the final results were integrated into Expression Atlas.
Article
Biochemical Research Methods
Manuel Bernal-Llinares et al.
Summary: Identifiers.org is a key tool for the annotation and cross-referencing of Life Science data, offering services to construct and resolve globally unique identifiers CID. They continuously improve services to support the growing demand, and deploy new infrastructure in a commercial cloud environment to provide high availability and low-latency services.
Article
Biochemistry & Molecular Biology
Alex Bateman et al.
Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Nuno Bandeira et al.
Summary: The increase in clinical proteomics studies has raised concerns about managing and disseminating potentially sensitive human proteomics data. Balancing data privacy with efficient use and reuse of research efforts through sharing clinical proteomics data will require development efforts at different levels including bioinformatics infrastructure, policymaking, and mechanisms of oversight.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Editorial Material
Multidisciplinary Sciences
Thomas M. Keane et al.
Summary: This commentary discusses the current best practices and future perspectives for responsible handling of clinical proteomics and metabolomics data, emphasizing the lack of bioinformatics resources available to manage access to sensitive human datasets in clinical studies.
NATURE COMMUNICATIONS
(2021)
Review
Multidisciplinary Sciences
Chengxin Dai et al.
Summary: The authors proposed a format and software pipeline for presenting and validating metadata of proteomics datasets, integrating them into ProteomeXchange repositories. They implemented MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets, aiming to improve reproducibility and facilitate reanalysis and integration of public proteomics datasets.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
J. A. Reales-Calderon et al.
Summary: Pseudomonas aeruginosa is a significant opportunistic human pathogen, and the study of its proteome is crucial for uncovering virulence factors and antibiotic resistance mechanisms. The construction of proteomic resources like PeptideAtlas enables targeted proteomics studies, system-wide observations, and cross-species observational studies.
JOURNAL OF PROTEOMICS
(2021)
Article
Multidisciplinary Sciences
Andrew F. Jarnuczak et al.
Summary: Utilizing 11 proteomics datasets from the PRIDE database, a reference expression map was constructed for 191 cancer cell lines and 246 clinical tumor samples, revealing unique peptides in tumor samples and highlighting the correlation between baseline expression in cell lines and tumors. Integration of proteomics and transcriptomics data showed a median correlation of 0.58 across cell lines, indicating that mRNA levels are often a poor predictor of changes in protein abundance. This study represents the first meta-analysis focusing on cancer-related public proteomics datasets, emphasizing the shortcomings and limitations of such studies.
Article
Biochemical Research Methods
Eric W. Deutsch et al.
Summary: The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding virtual paths to mass spectra in public repositories, enabling greater transparency and traceability of spectral evidence. Over 1 billion USI identifications from more than 3 billion spectra are already available through ProteomeXchange repositories, supporting the findings of mass spectrometry proteomics studies.
Article
Biochemistry & Molecular Biology
Matthias Mann et al.
Summary: The rapid growth of biomedical data generation and computational capabilities has led to advancements in utilizing machine learning and deep learning in proteomics for predictive modeling and biomarker discovery. These technologies are essential for improving analytical workflows and integrating multi-omics data, while also raising concerns about model transparency, explainability, and data privacy when deploying MS-based biomarkers in clinical settings.
Article
Biochemistry & Molecular Biology
Klaas J. van Wijk et al.
Summary: The Arabidopsis PeptideAtlas is a resource that addresses key questions about the Arabidopsis thaliana proteome by analyzing published mass spectrometry data and providing reliable information about specific proteins. It identifies additional proteins and isoforms not currently in Araport11, evaluates physicochemical protein properties, and integrates with community resources for global access. The resource allows for targeted identification of unobserved proteins and serves as a platform for future incorporation of millions more MS/MS data.
Article
Biochemistry & Molecular Biology
Marie A. Brunet et al.
Summary: OpenProt is the first proteogenomic resource that supports a polycistronic annotation model for eukaryotic genomes, providing deeper annotation of open reading frames (ORFs) with supporting evidence from experimental data. The platform re-analyzes ribosome profiling and mass spectrometry datasets to report non-AUG initiation starts and control the unicity of detected peptides. In addition, detectability statistics and protein relationships are now reported for each protein, and a data analysis platform is offered for users to submit their datasets for analysis and access the results.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Spectroscopy
Lindsay K. Pino et al.
MASS SPECTROMETRY REVIEWS
(2020)
Article
Biochemistry & Molecular Biology
Xinhao Shao et al.
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biotechnology & Applied Microbiology
David Ochoa et al.
NATURE BIOTECHNOLOGY
(2020)
Article
Biochemical Research Methods
Pathmanaban Ramasamy et al.
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Biochemical Research Methods
Meena Choi et al.
Article
Multidisciplinary Sciences
Mukul K. Midha et al.
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Subash Adhikari et al.
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Yuki Moriya et al.
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biotechnology & Applied Microbiology
Georg Kustatscher et al.
NATURE BIOTECHNOLOGY
(2019)
Article
Multidisciplinary Sciences
Yasset Perez-Riverol et al.
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Pieter-Jan Volders et al.
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Wenguang Shao et al.
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemical Research Methods
Vagisha Sharma et al.
MOLECULAR & CELLULAR PROTEOMICS
(2018)
Article
Biochemistry & Molecular Biology
Mingxun Wang et al.
Article
Biochemistry & Molecular Biology
Shujiro Okuda et al.
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Eric W. Deutsch et al.
NUCLEIC ACIDS RESEARCH
(2017)
Review
Biochemical Research Methods
Eric W. Deutsch et al.
JOURNAL OF PROTEOME RESEARCH
(2017)
Article
Biochemical Research Methods
Juan Antonio Vizcaino et al.
MOLECULAR & CELLULAR PROTEOMICS
(2017)
Article
Biochemical Research Methods
Yasset Perez-Riverol et al.
MOLECULAR & CELLULAR PROTEOMICS
(2016)
Article
Biochemistry & Molecular Biology
Volodimir Olexiouk et al.
NUCLEIC ACIDS RESEARCH
(2016)
Article
Multidisciplinary Sciences
Mark D. Wilkinson et al.
Review
Computer Science, Information Systems
Eric W. Deutsch et al.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2015)
Article
Biochemical Research Methods
Johannes Griss et al.
MOLECULAR & CELLULAR PROTEOMICS
(2014)
Letter
Biotechnology & Applied Microbiology
Juan A. Vizcaino et al.
NATURE BIOTECHNOLOGY
(2014)
Article
Biochemistry & Molecular Biology
Kimberly A. Tryka et al.
NUCLEIC ACIDS RESEARCH
(2014)
Article
Biochemical Research Methods
Seungjin Na et al.
MOLECULAR & CELLULAR PROTEOMICS
(2012)
Article
Biochemical Research Methods
Terry Farrah et al.
Article
Biochemical Research Methods
Lennart Martens et al.
MOLECULAR & CELLULAR PROTEOMICS
(2011)
Review
Biochemistry & Molecular Biology
Eric W. Deutsch et al.
Article
Biochemical Research Methods
R Craig et al.
JOURNAL OF PROTEOME RESEARCH
(2004)