Changes between Version 11 and Version 12 of CreatingAnnotion
- Timestamp:
- 06/26/2018 04:51:01 PM (4 years ago)
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CreatingAnnotion
v11 v12 1 = Steps to Create a GRITS Project Archive = 1 2 The GRITS plugin "org.grits.toolbox.importer.ms.annotation.glycan.simiansearch" executes a tool title GELATO, which annotates MS spectra with candidate glycans from a specified database. The GELATO plugin is "org.grits.toolbox.ms.annotation". This plugin creates an archive that is readable by the GRITS GUI component (plugins "org.grits.toolbox.entry.ms.annotation" and "org.grits.toolbox.entry.ms.annotation.glycan"). While GELATO's algorithms perform the matching of peaks in MS spectra to glycans, the archive that is created is an instance of the GRITS MS object model (plugin "org.grits.toolbox.ms.om"). In order to extend GRITS to other forms of MS data, it will be helpful to understand the requirements for creation of an archive file that can be opened in GRITS. This document is meant to serve that purpose. 2 3 3 Minimal steps to create a GRITS MS Glycan Annotation archive. 4 == Minimal steps to create a GRITS MS Glycan Annotation archive == 4 5 5 6 Step one: populating the data structures with MS data. … … 10 11 Assuming a Direct Infusion experiment, the minimum data for GELATO is: 11 12 12 1) Creating Test Data 13 == Populating the Scan Data == 14 1) Adding MS Data 13 15 a) Create an MS1 scan (example code) 14 16 {{{ … … 58 60 }}} 59 61 60 2) Creating Test Glycan Objects 62 == Initialize Glycan Database == 63 2) Creating Glycan Objects 61 64 a) *** You must first initialize the EuroCarbDB GlycanBuilder BuilderWorkspace even though you never use the instance 62 65 {{{ … … 80 83 }}} 81 84 85 == Storing the User-specified Parameters == 82 86 3) Create Method object and populate with applicable settings 83 87 {{{ … … 110 114 }}} 111 115 116 == Data objects == 112 117 4) Create Data and DataHeader objects 113 118 {{{ … … 121 126 }}} 122 127 128 == Create Parameter Sets for Use in Calculating Candidate Glycans/Fragments for Matching to MS Peaks == 123 129 5) Create AnalyteSettings object 124 130 {{{ … … 131 137 }}} 132 138 139 == Determine Adduct Options == 133 140 6) create list of adducts to consider 134 141 a) * Note that class GlycanPreDefinedOptions has static, pre-defined glycan-specific options (see comments) … … 164 171 }}} 165 172 173 == Set Project Path and File Names == 166 174 7) Set the final name of the archive 167 175 * Setting the archive name / paths is an important consideration. For LC-MS/MS data, it is different (needs an overview file)! … … 172 180 }}} 173 181 182 == Match Glycan Features to MS Peaks == 174 183 8) Process data to annotate spectra 175 184 a) This is a sample method to annotate a single MS/MS spectra to a specified glycan structure … … 223 232 }}} 224 233 234 == Write the GRITS Project Files == 225 235 9) Create the archive that will be read by GRITS 226 236 a) Populate the Scan Feature objects
