{"id":2,"date":"2014-07-04T23:40:52","date_gmt":"2014-07-04T23:40:52","guid":{"rendered":"http:\/\/www.grits-toolbox.org\/?page_id=2"},"modified":"2021-12-10T18:47:09","modified_gmt":"2021-12-10T17:47:09","slug":"sample-page","status":"publish","type":"page","link":"http:\/\/www.grits-toolbox.org\/","title":{"rendered":"Welcome"},"content":{"rendered":"<h2>GRITS Toolbox &#8211; A mass spec annotation software<\/h2>\n<p>GRITS Toolbox is a modular software suite for processing, annotating and archiving of glycomics data with a focus on MS data.The software allows users to upload their instrument MS data files in open file formats (either as <a href=\"http:\/\/tools.proteomecenter.org\/wiki\/index.php?title=Formats:mzXML\">mzXML<\/a> or <a href=\"http:\/\/www.psidev.info\/mzml_1_0_0%20\">mzML<\/a>) and annotated them\u00a0 using the integration annotation module <a title=\"Annotation using GRITS\" href=\"http:\/\/www.grits-toolbox.org\/?page_id=52\">Glycomics Elucidation and Annotation Tool<\/a> (GELATO). GRITS Toolbox can process different types of MS data including MS profiling data, MS\/MS data from direct infusion experiments, LC\/MS\/MS data and TIM data. To propose glycan structures as annotations GRITS Toolbox uses a set of databases which have been curated by experts using our <a href=\"http:\/\/glycomics.ccrc.uga.edu\/qrator\/\">Qrator<\/a> software. Automatically annotated data can than be reviewed by the user and annotation can be changed depending on the users expertise. If MSn data is available users can review the fragment annotation of these spectra as well and use them to refine the structure annotation. Results can be exported to Microsoft Excel files and post-processed with other software tools. It is also possible to study the annotations of multiple experiments side by side to see the changes in glycosylation between the samples. This kind of report can be exported to Microsoft Excel as well.<\/p>\n<p>&nbsp;<\/p>\n<h2>GRITS Toolbox &#8211; Archive for metadata<\/h2>\n<p>In addition to the processing, evaluation and browsing of the experimental data GRITS Toolbox can also be used to archive meta data along with the experiment data. This provides a way to archive an complete overview of the experiment rather than storing different parts of information in multiple locations which will make it complicated to find all pieces later. The metadata that can be handled by GRITS Toolbox are:<\/p>\n<ul>\n<li>Project management information (project description, collaboration partners, task list, milestones)<\/li>\n<li>Description of the sample including sample tracking, amount and QC information<\/li>\n<li>Description of the experiment performed with information about all protocols and their configuration<\/li>\n<li>Any file that should be associated with the project or sample (e.g. other types of experimental data, reports, papers, supplementary information)<\/li>\n<li>Emails related to the sample or project<\/li>\n<\/ul>\n<p>All information added to GRITS Toolbox can be downloaded from the software (e.g. files) or exported into reports (e.g. PDF or Word).<\/p>\n<p>&nbsp;<\/p>\n<h2>GRITS Toolbox &#8211; Availability<\/h2>\n<p>Best of all &#8211; GRITS toolbox is freely available for <a title=\"Downloads\" href=\"http:\/\/www.grits-toolbox.org\/?page_id=303\">download <\/a>from this webpage. However to be able to report usage to our funding agency we require that you provide an email address. Rest assure that we will not provide or sell your information.<\/p>\n<p>&nbsp;<\/p>\n<h2>GRITS Toolbox &#8211; Features<\/h2>\n<table border=\"0\" width=\"100%\">\n<tbody>\n<tr>\n<td width=\"32px\" style=\"vertical-align:top;\"><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=365#project\"><img decoding=\"async\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/05\/project32.png\" \/><\/a><\/td>\n<td><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=365#project\">Project management<\/a><br \/>\nManagement and arching of project information (collaboration partners, tasks, milestones).<\/td>\n<td width=\"32px\" style=\"vertical-align:top;\"><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=365#sample\"><img decoding=\"async\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/05\/sample32.png\" \/><\/a><\/td>\n<td><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=365#sample\">Sample management<\/a><br \/>\nStoring metadata describing our sample or set of samples used for an experiment.<\/td>\n<td width=\"32px\" style=\"vertical-align:top;\"><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=365#experiment\"><img decoding=\"async\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/05\/experiment32.png\" \/><\/a><\/td>\n<td><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=365#experiment\">Experiment design<\/a><br \/>\nStoring of metadata describing the experiment performed including all the protocols used.<\/td>\n<\/tr>\n<tr>\n<td width=\"32px\" style=\"vertical-align:top;\"><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#msdata\"><img decoding=\"async\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/05\/ms32.png\" \/><\/a><\/td>\n<td><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#msdata\">Mass spec data<\/a><br \/>\nUpload and browsing of mass spectrometric instrument data using mzXML and mzML files.<\/td>\n<td width=\"32px\" style=\"vertical-align:top;\"><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#msannotation\"><img decoding=\"async\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/05\/gelato32.png\" \/><\/a><\/td>\n<td><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#msannotation\">(Semi-)automated annotation<\/a><br \/>\nAnnotation of glycomics MS data using the GELATO annotation algorithm and integrated human curated glycan databases.<\/td>\n<td width=\"32px\" style=\"vertical-align:top;\"><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#cartoonstyle\"><img decoding=\"async\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/05\/annotation32.png\" \/><\/a><\/td>\n<td><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#cartoonstyle\">Cartoon representation<\/a><br \/>\nGlycan annotations and fragment annotations can be displayed in different cartoon representations and IUPAC like text representation.<\/td>\n<\/tr>\n<tr>\n<td width=\"32px\" style=\"vertical-align:top;\"><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#msnannotation\"><img decoding=\"async\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/05\/annotation32.png\" \/><\/a><\/td>\n<td><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#msnannotation\">MSn annotation<\/a><br \/>\nMSn data can be annotated and each MS level can be studied in detail comparing the different candidate annotations.<\/td>\n<td width=\"32px\" style=\"vertical-align:top;\"><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#msspectra\"><img decoding=\"async\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/05\/annotation32.png\" \/><\/a><\/td>\n<td><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#msspectra\">Spectrum annotation<\/a><br \/>\nGlycan annotations or fragment annotations can be rendered on top of an MS spectra for visual inspection of results.<\/td>\n<td width=\"32px\" style=\"vertical-align:top;\"><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#merge\"><img decoding=\"async\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/05\/merge32.png\" \/><\/a><\/td>\n<td><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=363#merge\">Side-by-side comparison<\/a><br \/>\nMS annotations from different samples can be compared side-by-side to see changes in glycosylation or glycan expression.<\/td>\n<\/tr>\n<tr>\n<td width=\"32px\" style=\"vertical-align:top;\"><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=365#archive\"><img decoding=\"async\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/05\/archive32.png\" \/><\/a><\/td>\n<td><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=365#archive\">Document archive<\/a><br \/>\nIn addition to the data and metadata any type of file or email can be archive with the project or sample.<\/td>\n<td width=\"32px\" style=\"vertical-align:top;\"><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=376\"><img decoding=\"async\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/05\/eclipse32.png\" \/><\/a><\/td>\n<td><a href=\"http:\/\/www.grits-toolbox.org\/?page_id=376\">Modular software system<\/a><br \/>\nGRITS Toolbox is bases on the well known framework Eclipse can be extended by third party plugins.<\/td>\n<td width=\"32px\" style=\"vertical-align:top;\"><\/td>\n<td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"<p>GRITS Toolbox &#8211; A mass spec annotation software GRITS Toolbox is a modular software suite for processing, annotating and archiving of glycomics data with a focus on MS data.The software allows users to upload their instrument MS data files in open file formats (either as mzXML or mzML) and annotated them\u00a0 using the integration annotation [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"_exactmetrics_skip_tracking":false,"_exactmetrics_sitenote_active":false,"_exactmetrics_sitenote_note":"","_exactmetrics_sitenote_category":0,"footnotes":""},"_links":{"self":[{"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=\/wp\/v2\/pages\/2"}],"collection":[{"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2"}],"version-history":[{"count":17,"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=\/wp\/v2\/pages\/2\/revisions"}],"predecessor-version":[{"id":422,"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=\/wp\/v2\/pages\/2\/revisions\/422"}],"wp:attachment":[{"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}