GRITS Toolbox – 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 using the integration annotation module Glycomics Elucidation and Annotation Tool (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 Qrator 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.
GRITS Toolbox – Archive for metadata
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:
- Project management information (project description, collaboration partners, task list, milestones)
- Description of the sample including sample tracking, amount and QC information
- Description of the experiment performed with information about all protocols and their configuration
- Any file that should be associated with the project or sample (e.g. other types of experimental data, reports, papers, supplementary information)
- Emails related to the sample or project
All information added to GRITS Toolbox can be downloaded from the software (e.g. files) or exported into reports (e.g. PDF or Word).
GRITS Toolbox – Availability
Best of all – GRITS toolbox is freely available for download 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.
GRITS Toolbox – Features
Management and arching of project information (collaboration partners, tasks, milestones).
Storing metadata describing our sample or set of samples used for an experiment.
Storing of metadata describing the experiment performed including all the protocols used.
|Mass spec data
Upload and browsing of mass spectrometric instrument data using mzXML and mzML files.
Annotation of glycomics MS data using the GELATO annotation algorithm and integrated human curated glycan databases.
Glycan annotations and fragment annotations can be displayed in different cartoon representations and IUPAC like text representation.
MSn data can be annotated and each MS level can be studied in detail comparing the different candidate annotations.
Glycan annotations or fragment annotations can be rendered on top of an MS spectra for visual inspection of results.
MS annotations from different samples can be compared side-by-side to see changes in glycosylation or glycan expression.
In addition to the data and metadata any type of file or email can be archive with the project or sample.
|Modular software system
GRITS Toolbox is bases on the well known framework Eclipse can be extended by third party plugins.