The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive ...(http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development 'PRIDE Cluster' and 'PRIDE Proteomes', which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive.
The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based ...proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.
Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average 75% of spectra analysed in an MS experiment remain unidentified. We propose to use spectrum clustering ...at a large-scale to shed a light on these unidentified spectra. PRoteomics IDEntifications database (PRIDE) Archive is one of the largest MS proteomics public data repositories worldwide. By clustering all tandem MS spectra publicly available in PRIDE Archive, coming from hundreds of datasets, we were able to consistently characterize three distinct groups of spectra: 1) incorrectly identified spectra, 2) spectra correctly identified but below the set scoring threshold, and 3) truly unidentified spectra. Using a multitude of complementary analysis approaches, we were able to identify less than 20% of the consistently unidentified spectra. The complete spectrum clustering results are available through the new version of the PRIDE Cluster resource (http://www.ebi.ac.uk/pride/cluster). This resource is intended, among other aims, to encourage and simplify further investigation into these unidentified spectra.
The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that ...the tool had some limitations and could not handle several user requirements that were now becoming commonplace. This prompted us to design and implement a whole new suite of tools that would build on the successes of the original PRIDE Converter and allow users to generate submission-ready, well-annotated PRIDE XML files. The PRIDE Converter 2 tool suite allows users to convert search result files into PRIDE XML (the format needed for performing submissions to the PRIDE database), generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra, or by merging several PRIDE XML files together. All the tools have both a graphical user interface that provides a dialog-based, user-friendly way to convert and prepare files for submission, as well as a command-line interface that can be used to integrate the tools into existing or novel pipelines, for batch processing and power users. The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MS-proteomics data repositories.
The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or ...already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE.
The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX “complete” submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/.
A avifauna do estado do Tocantins foi inicialmente sumarizada a partir das coleções ornitológicas conduzidas por José Hidasi, entre as décadas de 1960 e 1990, sendo recompiladas em 2009. Após 15 ...anos, apresentamos uma nova listagem das espécies de aves ocorrentes no estado, considerando riqueza e composição, status migratório, perfil de endemismo, estado de conservação e aspectos biogeográficos. Ao todo, foram listadas 720 espécies, das quais 699 (97%) apresentaram evidência documental de ocorrência no Tocantins (lista primária), enquanto 21 (3%) foram avistadas e/ou ouvidas (lista secundária), representando 36,6% da avifauna reconhecida para o Brasil. Outras 72 espécies foram descartadas para o Tocantins (lista terciária). Ainda referente às 720 espécies, 48 são consideradas endemismos brasileiros, 31 são migrantes continentais neárticos e cinco, migrantes austrais, enquanto 43 estão em alguma categoria de ameaça de extinção em âmbito global ou nacional. A simpatria de aves típicas da Amazônia e do Cerrado reflete o caráter ecotonal da avifauna do estado, que ainda abriga, pontualmente, espécies típicas da Caatinga e da Mata Atlântica, e anseia pela descrição de uma presumida nova espécie do gênero Certhiaxis. Finalmente, a listagem apresentada designa-se como base inicial para elaboração de uma lista estadual de aves ameaçadas de extinção.
Because of the patchiness of their habitat, its perceived low conservation value, and tendency to burn, bamboo-specialist birds are vulnerable to habitat loss. We documented the habitat use and ...foraging strategies ofCeleus obrieni, Kaempfer's Woodpecker, in forestedcerrado(savanna) with patches of the bambooGuadua paniculatanear Pium, Tocantins, Brazil. We surveyed forC. obrieni, measured vegetation structure at 30 sites where it was detected and 23 where it was not detected, then compared vegetation characteristics through nonmetric multidimentional scaling and one-way analysis of similarity to determine whetherC. obrieniwas specializing on particular habitat characteristics. We studied the species' foraging and compared the abundance of prey in drilled and nondrilled stems to evaluate its dietary specialization. All sites withC. obrienihad large, tall stands ofG. paniculata, indicating habitat specialization. Drilling most frequently on large, dry stems from 2 to 4 m off the ground, the woodpeckers consumed ants, mainlyCamponotus depressusandAzteca fasciata, which colonize the internodes of bamboo stems. Habitat specialists are more vulnerable to habitat loss or alteration but can serve as indicator species for the reaching of conservation goals. Large stands of forestedcerradowith patches of bamboo should be conserved forC. obrienito be maintained. The patchiness of bamboo forest may impede dispersal ofC. obrieni.
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