Changes between Version 11 and Version 12 of CreatingAnnotion


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Timestamp:
06/26/2018 04:51:01 PM (3 years ago)
Author:
dbrentw
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  • CreatingAnnotion

    v11 v12  
     1= Steps to Create a GRITS Project Archive =
    12The 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.
    23
    3 Minimal steps to create a GRITS MS Glycan Annotation archive.
     4== Minimal steps to create a GRITS MS Glycan Annotation archive ==
    45
    56Step one:  populating the data structures with MS data.
     
    1011Assuming a Direct Infusion experiment, the minimum data for GELATO is:
    1112
    12 1) Creating Test Data
     13== Populating the Scan Data ==
     141) Adding MS Data
    1315  a) Create an MS1 scan (example code)
    1416{{{
     
    5860}}}
    5961
    60 2) Creating Test Glycan Objects
     62== Initialize Glycan Database ==
     632) Creating Glycan Objects
    6164  a) *** You must first initialize the EuroCarbDB GlycanBuilder BuilderWorkspace even though you never use the instance
    6265{{{
     
    8083}}}
    8184
     85== Storing the User-specified Parameters ==
    82863) Create Method object and populate with applicable settings
    8387{{{
     
    110114}}}
    111115
     116== Data objects ==
    1121174) Create Data and DataHeader objects
    113118{{{
     
    121126}}}
    122127
     128== Create Parameter Sets for Use in Calculating Candidate Glycans/Fragments for Matching to MS Peaks ==
    1231295) Create AnalyteSettings object
    124130{{{
     
    131137}}}
    132138
     139== Determine Adduct Options ==
    1331406) create list of adducts to consider
    134141  a) * Note that class GlycanPreDefinedOptions has static, pre-defined glycan-specific options (see comments)
     
    164171}}}
    165172
     173== Set Project Path and File Names ==
    1661747) Set the final name of the archive
    167175  * Setting the archive name / paths is an important consideration. For LC-MS/MS data, it is different (needs an overview file)!
     
    172180}}}
    173181
     182== Match Glycan Features to MS Peaks ==
    1741838) Process data to annotate spectra
    175184  a) This is a sample method to annotate a single MS/MS spectra to a specified glycan structure
     
    223232}}}
    224233
     234== Write the GRITS Project Files ==
    2252359) Create the archive that will be read by GRITS
    226236  a) Populate the Scan Feature objects