{"id":363,"date":"2016-04-29T18:02:15","date_gmt":"2016-04-29T16:02:15","guid":{"rendered":"http:\/\/www.grits-toolbox.org\/?page_id=363"},"modified":"2021-12-09T14:57:16","modified_gmt":"2021-12-09T13:57:16","slug":"massspec-features","status":"publish","type":"page","link":"http:\/\/www.grits-toolbox.org\/?page_id=363","title":{"rendered":"Glycomics mass spectrometry"},"content":{"rendered":"<div style=\"border: 0px solid; width: 100%; clear: both; height: 368px;\">\n<p><a name=\"msdata\" href=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-ms-data.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignleft wp-image-338\" title=\"MS data uploaded to GRITS Toolbox\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-ms-data.png\" alt=\"feature-ms-data\" width=\"450\" height=\"363\" \/><\/a><\/p>\n<div style=\"position: relative; top: 50%; transform: translateY(-50%); margin-left: 470px;\">\n<h4>MS data management<\/h4>\n<p>MS data from different types of experiments(e.g. MS profile, direct infusion MS\/MS, LC\/MS\/MS, Total Ion Mapping) can be uploaded using mzXML or mzML. The uploaded data can review in GRITS Toolbox:<\/p>\n<ul>\n<li>list all uploaded file and associated meta data. Files can also be saved back to the file system.<\/li>\n<li>view MS spectra<\/li>\n<li>browse and traverse the MS scan list if the experiment consists of more than one MS scan<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<div style=\"border: 0px solid; width: 100%; clear: both; height: 368px;\">\n<p><a name=\"msannotation\" href=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-annotation.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-334\" title=\"Annotation of a direct infusion experiment\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-annotation.png\" alt=\"feature-annotation\" width=\"450\" height=\"363\" \/><\/a><\/p>\n<div style=\"position: relative; top: 50%; transform: translateY(-50%); margin-right: 470px;\">\n<h4>Annotation of glycomics MS data<\/h4>\n<p>Glycomics MS data can be automatically annotated using the integrated annotation module (GELATO). Annotated data can than be displayed and reviewed by the user:<\/p>\n<ul>\n<li>each precursor peak (or MS peak for MS profiling) will be annotated with a set of structures matching the m\/z<\/li>\n<li>users can select the right structures from the candidate set<\/li>\n<li>a large diversity of complimentary information is provided with each annotation to support users in choosing the right candidate<\/li>\n<\/ul>\n<p>The annotation table can also be exported to Excel allowing for external data processing and data analysis.<\/p>\n<\/div>\n<\/div>\n<div style=\"border: 0px solid; width: 100%; clear: both; height: 293px;\">\n<p><a name=\"cartoonstyle\" href=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-cartoon-style.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignleft wp-image-336\" title=\"Different graphical representations supported by GRITS Toolbox\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-cartoon-style.png\" alt=\"feature-cartoon-style\" width=\"450\" height=\"288\" \/><\/a><\/p>\n<div style=\"position: relative; top: 50%; transform: translateY(-50%); margin-left: 470px;\">\n<h4>Graphical glycan representation<\/h4>\n<p>GRITS Toolbox supports several different glycan representations allowing users to choose their favored way of displaying glycans:<\/p>\n<ul>\n<li>cartoon representation according to the &#8220;<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/books\/NBK1931\/figure\/ch1.f5\/?report=objectonly\">Essentials of GlycoBiology<\/a>&#8220;<\/li>\n<li>cartoon representation developed by the Oxford Glycoscience group<\/li>\n<li>textual representation similar to the <a href=\"http:\/\/www.chem.qmul.ac.uk\/iupac\/2carb\/\">recommendation developed by the IUPAC<\/a><\/li>\n<\/ul>\n<\/div>\n<\/div>\n<div style=\"border: 0px solid; width: 100%; clear: both; height: 368px;\">\n<p><a name=\"msnannotation\" href=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-ms-ms.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-340\" title=\"Side by side comparision of glycan candidates for a MS2 spectra\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-ms-ms.png\" alt=\"feature-ms-ms\" width=\"450\" height=\"363\" \/><\/a><\/p>\n<div style=\"position: relative; top: 50%; transform: translateY(-50%); margin-right: 470px;\">\n<h4>Annotation of MSn data<\/h4>\n<p>GRITS Toolbox allows the visualization of MSn data by comparing candidate structures and their fragments side by side:<\/p>\n<ul>\n<li>all possible fragmentation annoation of a candidate structure for a MSn spectra are shown<\/li>\n<li>users can select the right structures from the candidate set<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<div style=\"border: 0px solid; width: 100%; clear: both; height: 368px;\">\n<p><a name=\"msspectra\" href=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-annotated-spectrum.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignleft wp-image-333\" title=\"Annotation of MS spectra\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-annotated-spectrum.png\" alt=\"feature-annotated-spectrum\" width=\"450\" height=\"363\" \/><\/a><\/p>\n<div style=\"position: relative; top: 50%; transform: translateY(-50%); margin-left: 470px;\">\n<h4>Graphical annotation of MS spectra<\/h4>\n<p>Structure annotations or fragment annotation can be rendered on top of a MS spectra plot to allow visual inspection of the annotation:<\/p>\n<ul>\n<li>controls on top of the plot allow customizing the display<\/li>\n<li>for MSn annotation users can scroll through the candidates and see how annotation changes with each candidate<\/li>\n<li>selection of the right candidate can be changed<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<div style=\"border: 0px solid; width: 100%; clear: both; height: 356px;\">\n<p><a name=\"merge\" href=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-ms-merge.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-339\" title=\"Side by side comparison of annotations from different samples\" src=\"http:\/\/www.grits-toolbox.org\/wp-content\/uploads\/2016\/04\/feature-ms-merge.png\" alt=\"feature-ms-merge\" width=\"450\" height=\"351\" \/><\/a><\/p>\n<div style=\"position: relative; top: 50%; transform: translateY(-50%); margin-right: 470px;\">\n<h4>Comparing annotations from different samples<\/h4>\n<p>Finally, annotations from different samples can be shown side by side to allow studying changes in glycosylation of the different samples:<\/p>\n<ul>\n<li>for each sample the user selected annotation are shown<\/li>\n<li>annotations are aligned based on their m\/z value<\/li>\n<li>additional information (for example: intensity, relative intensity, intensity towards a standard etc.) can be added to the report<\/li>\n<\/ul>\n<p>The report can be exported to Excel for further data processing and data analysis.\n<\/p><\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>MS data management MS data from different types of experiments(e.g. MS profile, direct infusion MS\/MS, LC\/MS\/MS, Total Ion Mapping) can be uploaded using mzXML or mzML. The uploaded data can review in GRITS Toolbox: list all uploaded file and associated meta data. Files can also be saved back to the file system. view MS spectra [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":74,"parent":344,"menu_order":1,"comment_status":"closed","ping_status":"closed","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\/363"}],"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=363"}],"version-history":[{"count":11,"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=\/wp\/v2\/pages\/363\/revisions"}],"predecessor-version":[{"id":392,"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=\/wp\/v2\/pages\/363\/revisions\/392"}],"up":[{"embeddable":true,"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=\/wp\/v2\/pages\/344"}],"wp:featuredmedia":[{"embeddable":true,"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=\/wp\/v2\/media\/74"}],"wp:attachment":[{"href":"http:\/\/www.grits-toolbox.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=363"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}