{"id":8038,"date":"2016-03-21T07:00:13","date_gmt":"2016-03-21T11:00:13","guid":{"rendered":"http:\/\/admin.acceleratingscience.com\/?p=8038"},"modified":"2016-04-29T16:53:02","modified_gmt":"2016-04-29T16:53:02","slug":"upgrades-and-more-for-pride-inspector-toolsuite","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/proteomics\/upgrades-and-more-for-pride-inspector-toolsuite\/","title":{"rendered":"Upgrades and More for PRIDE Inspector Toolsuite"},"content":{"rendered":"<p><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/admin.acceleratingscience.com\/proteomics\/wp-content\/uploads\/sites\/2\/2016\/03\/shutterstock_103848494.jpg\" style=\"float: left;margin: 10px\" alt=\"Data visualization. Image: ivn3da\/Shutterstock.com\" width=\"330\" height=\"330\" \/>The latest incarnation of the PRIDE Inspector T<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">oolsuite<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;updates the original resource to bring extra functionality to proteomics researchers.<sup>1<\/sup>&nbsp;Described by Perez-<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">Riverol<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;et al. (2016) as representing &ldquo;a feasible way to visualize annotated spectra coming from a wide variety of tools,&rdquo; the latest release handles all the various stages of proteomics research from original data analysis to supporting complete&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">ProteomeXchange<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;submissions.&nbsp;&nbsp;<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><\/p>\n<p><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">Developed in association with&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">the&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">PRIDE<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">(<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">PRoteomics<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">IDEntifications<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">)<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">database<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">, the&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">ProteomeXch<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">a<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">n<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">ge<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;consortium and&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">HUPO&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">PSI&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">(Proteomics Standards Initiative)&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">guiding principles, the new version of the PRIDE Inspector tool kit has been extensively upgraded in response to changes in mass spectrometry&ndash;based proteomics methodology and<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;feedback from tool user requests. The&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">software<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">was developed<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;originally to overcome problems encountered by researchers in accessing different file formats and to enable data visualization across studies. The fresh upgrade continues this direction and adds further functionality.<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><\/p>\n<p><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">The programs&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">are written<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;in Java and work with a number of different operating systems, including Microsoft Windows, Mac OS and Linux. Each module remains a stand-alone tool for interchangeability and independence. As with the previous&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">tool suite<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">, the upgraded package&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">is&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">distributed<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;as<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;open source&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">and is available under a permissive Apache&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">Licence<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;v.2. It is&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">accessible for download from GitHub.<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><\/p>\n<p><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">The resources group into two main libraries:<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><\/p>\n<ul>\n<li><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">PRIDE-Utilities: data handling, validation tools and quality assurance<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><\/li>\n<li><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">PRIDE-<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">Toolsuite:<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;graphical user interface components and tools<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><\/li>\n<\/ul>\n<p><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">The tool also includes a user handbook and some example files for guidance.<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><\/p>\n<p><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">According to Perez-<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">Riverol<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;et al., the upgraded version has many advances, including support for new file formats like&nbsp;<span class=\"thread\"><\/span><\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">mzIdentML<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">, an improved user interface, metadata overview, and support for identification and quantitation results in&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">mzTab<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;files.&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">Enhanced functionality visualizes protein and peptide information, mass spectrum fragment annotations, and quantitative data. In addition, t<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">he&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">tool suite<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">can<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;create summary charts for users and export analysis to&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">mzTab<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;format. It can also access and search the PRIDE archive. The authors describe this functionality as &ldquo;comprehensive capture and reporting.&rdquo;<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><\/p>\n<p><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">Summarizing the updated PRIDE Inspector&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">Toolsuite<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">, Perez-<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">Riverol<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;et al. note that it supports current major PSI standard file formats. The programs handle quantitative data through the&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">mzTab<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;format and provide a better quality assurance workflow. Finally, the updated version is still capable of further refinement: the build is such that developers are able to add new features and possibly&nbsp;<\/span><\/span><span class=\"thread\"><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">integrate<\/span><\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;the&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">tool suite<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;with laboratory information management systems (LIMS) for an enhanced research experience.<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><\/p>\n<p><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\"><\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><\/p>\n<p><strong><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">Reference<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><\/strong><\/p>\n<p><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">1. &nbsp;Perez-Riverol, Y., et al. (2016) &#8220;<\/span><\/span><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26545397\" target=\"_blank\"><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">PRIDE Inspector&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">Toolsuite<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">: Moving toward a<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;u<\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">niversal visualization tool for proteomics<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;d<\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">ata standard formats and quality a<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">ssessment of&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"SpellingError SCX164523056\">ProteomeXchange<\/span><\/span><\/a><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\"><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26545397\" target=\"_blank\">&nbsp;datasets<\/a>,&#8221;&nbsp;<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">Molecular<\/span><\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">&nbsp;&amp; Cellular<\/span><\/span><span class=\"EOP SCX164523056\">&nbsp;<\/span><span class=\"TextRun SCX164523056\"><span class=\"NormalTextRun SCX164523056\">Proteomics, 15 (pp. 305&ndash;317), doi: 10.1074\/mcp.O115.050229<\/span><\/span><span class=\"EOP SCX164523056\"><br \/><\/span><\/p>\n<p><i>Post Author: Amanda Maxwell. Mixed media artist; blogger and social media communicator; clinical scientist and writer. A digital space explorer, engaging readers by translating complex theories and subjects creatively into everyday language.<\/i><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The latest incarnation of the PRIDE Inspector Toolsuite&nbsp;updates the original resource to bring extra functionality to proteomics researchers.1&nbsp;Described by Perez-Riverol&nbsp;et al. (2016) as representing &ldquo;a feasible way to visualize annotated spectra coming from a wide variety of tools,&rdquo; the latest release handles all the various stages of proteomics research from original data analysis to supporting<\/p>\n","protected":false},"author":21,"featured_media":8037,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[317],"tags":[814],"division":[],"class_list":{"0":"post-8038","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-bioinformatics-proteomics","8":"tag-computational-proteomics","9":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"<!-- 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