Dataset Information

From Peptidome to PRIDE: public proteomics data migration at a large scale.

ABSTRACT: The PRIDE database, developed and maintained at the European Bioinformatics Institute (EBI), is one of the most prominent data repositories dedicated to high throughput MS-based proteomics data. Peptidome, developed by the National Center for Biotechnology Information (NCBI) as a sibling resource to PRIDE, was discontinued due to funding constraints in April 2011. A joint effort between the two teams was started soon after the Peptidome closure to ensure that data were not "lost" to the wider proteomics community by exporting it to PRIDE. As a result, data in the low terabyte range have been migrated from Peptidome to PRIDE and made publicly available under experiment accessions 17 900-18 271, representing 54 projects, ~53 million mass spectra, ~10 million peptide identifications, ~650,000 protein identifications, ~1.1 million biologically relevant protein modifications, and 28 species, from more than 30 different labs.

SUBMITTER: Csordas A

PROVIDER: S-EPMC3717177 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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From Peptidome to PRIDE: public proteomics data migration at a large scale.

Csordas Attila A Wang Rui R Ríos Daniel D Reisinger Florian F Foster Joseph M JM Slotta Douglas J DJ Vizcaíno Juan Antonio JA Hermjakob Henning H

Proteomics 20130420 10-11

The PRIDE database, developed and maintained at the European Bioinformatics Institute (EBI), is one of the most prominent data repositories dedicated to high throughput MS-based proteomics data. Peptidome, developed by the National Center for Biotechnology Information (NCBI) as a sibling resource to PRIDE, was discontinued due to funding constraints in April 2011. A joint effort between the two teams was started soon after the Peptidome closure to ensure that data were not "lost" to the wider pr ...[more]

PMID: 23533138

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Project description:BackgroundPhosphorylation is the most prevalent post-translational modification on eukaryotic proteins. Multisite phosphorylation enables a specific combination of phosphosites to determine the speed, specificity and duration of biological response. Until recent years, the lack of high quality data limited the possibility for analyzing the properties of phosphorylation at the proteome scale and in the context of a wide range of conditions. Thanks to advances of mass spectrometry technologies, thousands of phosphosites from in-vivo experiments were identified and archived in the public domain. Such resource is appropriate to derive an unbiased view on the phosphosites properties in eukaryotes and on their functional relevance.ResultsWe present statistically rigorous tests on the spatial and functional properties of a collection of approximately 70,000 reported phosphosites. We show that the distribution of phosphosites positioning along the protein tends to occur as dense clusters of Serine/Threonines (pS/pT) and between Serine/Threonines and Tyrosines, but generally not as much between Tyrosines (pY) only. This phenomenon is more ubiquitous than anticipated and is pertinent for most eukaryotic proteins: for proteins with > or = 2 phosphosites, 54% of all pS/pT sites are within 4 amino acids of another site. We found a strong tendency for clustered pS/pT to be activated by the same kinase. Large-scale analyses of phosphopeptides are thus consistent with a cooperative function within the cluster.ConclusionsWe present evidence supporting the notion that clusters of pS/pT but generally not pY should be considered as the elementary building blocks in phosphorylation regulation. Indeed, closely positioned sites tend to be activated by the same kinase, a signal that overrides the tendency of a protein to be activated by a single or only few kinases. Within these clusters, coordination and positional dependency is evident. We postulate that cellular regulation takes advantage of such design. Specifically, phosphosite clusters may increase the robustness of the effectiveness of phosphorylation-dependent response.ReviewersReviewed by Joel Bader, Frank Eisenhaber, Emmanuel Levy (nominated by Sarah Teichmann). For the full reviews, please go to the Reviewers' comments section.

Project description:BackgroundVaccines are promising tools to control the spread of COVID-19. An effective vaccination campaign requires government policies and community engagement, sharing experiences for social support, and voicing concerns about vaccine safety and efficiency. The increasing use of online social platforms allows us to trace large-scale communication and infer public opinion in real time.ObjectiveThis study aimed to identify the main themes in COVID-19 vaccine-related discussions on Twitter in Japan and track how the popularity of the tweeted themes evolved during the vaccination campaign. Furthermore, we aimed to understand the impact of critical social events on the popularity of the themes.MethodsWe collected more than 100 million vaccine-related tweets written in Japanese and posted by 8 million users (approximately 6.4% of the Japanese population) from January 1 to October 31, 2021. We used Latent Dirichlet Allocation to perform automated topic modeling of tweet text during the vaccination campaign. In addition, we performed an interrupted time series regression analysis to evaluate the impact of 4 critical social events on public opinion.ResultsWe identified 15 topics grouped into the following 4 themes: (1) personal issue, (2) breaking news, (3) politics, and (4) conspiracy and humor. The evolution of the popularity of themes revealed a shift in public opinion, with initial sharing of attention over personal issues (individual aspect), collecting information from news (knowledge acquisition), and government criticism to focusing on personal issues. Our analysis showed that the Tokyo Olympic Games affected public opinion more than other critical events but not the course of vaccination. Public opinion about politics was significantly affected by various social events, positively shifting attention in the early stages of the vaccination campaign and negatively shifting attention later.ConclusionsThis study showed a striking shift in public interest in Japan, with users splitting their attention over various themes early in the vaccination campaign and then focusing only on personal issues, as trust in vaccines and policies increased. An interrupted time series regression analysis showed that the vaccination rollout to the general population (under 65 years) increased the popularity of tweets about practical advice and personal vaccination experience, and the Tokyo Olympic Games disrupted public opinion but not the course of the vaccination campaign. The methodology developed here allowed us to monitor the evolution of public opinion and evaluate the impact of social events on public opinion, using large-scale Twitter data.

Dataset Information

From Peptidome to PRIDE: public proteomics data migration at a large scale.

Publications

From Peptidome to PRIDE: public proteomics data migration at a large scale.

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