SimGlycan description
An inovative MS/MS data analysis tool.

SimGlycan predicts the structure of a glycan from the MS/MS data acquired by mass spectrometry, facilitating the study of glycosylation and post translational modifications studies.

SimGlycan accepts the experimental MS profiles generated by a mass spectrometer, matches them with its own database of theoretical fragmentation of over 8,000 glycans and generates a list of probable glycan structures.

Each structure is scored to reflect how closely it matches your experimental data. Other biological information for the probable glycan structures such as the glycan class, reaction, pathway and enzyme are also made available for easy reference. SimGlycan predicts the glycan structure, scores it and generates a list of probable glycans that closely match the your experimental MS profile saving you the time and the frustration of laborious work.

Here are some key features of "SimGlycan":

Robust Glycan Database
· The SimGlycan database is a large relational database populated with theoretical fragments of known glycan structures made up of 62 different monosaccharides. Every glycan in the database is fragmented for each of the possible fifty one reaction conditions using an intensive fragmentation algorithm. This ensures that the probable glycan fragments reported are comprehensive and accurate.
· Every effort has been made while populating this database to make it extremely high quality, enabling reliable data mining for future applications of glycobiology. SimGlycan database supports 8184 glycans, 5296 biological sources, 3774 glycan compositions, 5620 classes, 204 biochemical reactions, 150 biochemical pathways, 184 enzymes and 8143 database links.

Comprehensive Result Analysis
· For every probable glycan structure, SimGlycan provides glycan fragments, structure, sequence, composition, glycan mass, class, reaction, pathway, enzyme and other database links (CarbBank).
· SimGlycan accepts experimental m/z and intensity values of both released glycans and glycopeptides generated from a mass spectrometer. It allows you to specify the number of antennae, reducing terminal monosaccharide and non-reducing terminal monosaccharides expected for the structure, thereby enhancing the accuracy of the final search result. Acceptable file formats include simple text files, .xls files or the standard output file formats such as mzData and mzXML. No matter what make your instrument is, the output can be converted to these formats using third party tools. Other raw file formats such as wiff and t2d generated by mass spectrometers from Applied Biosystems, 4800 Plus MALDI TOF/TOF Analyzer, the 4000 QTRAP System and the QSTAR Elite System, are directly supported by the program.

Accurate Glycan Ranking
· All the possible glycan structures are ranked and scored based on our proprietary search and scoring algorithm. The ranking algorithm is based on calculating the glycan score, which is a numerical representation of how close the experimental mass of the glycan is to the mass of the glycans included in our database. The glycans with the same mass are then ranked in decreasing order of their intensities.
· A list of glycans along with their scores are displayed in the Search Results Pane. The highest rated glycan sequence is displayed at the top of the list. This glycan represents the most probable glycan structure followed by the rest in decreasing probability. Fragment nomenclature is based on the standard Domon Costello rules (1988) alongwith the rules described in Cooper et al. (1999)

Project Management
· SimGlycan provides a comprehensive project management, associating results with input profile and search parameters. You can open any number of projects. Each project can include up to 10 MS profiles. The projects can be classified on the basis of the source, the lab or the research goal. This is important, especially when conducting large scale projects.
· You can access glycan related information at the click of a button. Unlike web based applications, SimGlycan saves it on your own computer.

Glycan Structure:
· Displays the molecular structure (carbohydrate sequence) of the glycan.

Glycan Fragments:
· Displays the nomenclature, structure, m/z value and mass using Domon Costello rules of fragmentation. A serial number is assigned to each fragment.

Generate Report:
· You can create a comprehensive glycan search report for your lab notebook, publication or sharing information with your colleagues. The report includes the glycan characteristics such as the ID, sequence, name, composition, mass, precursor ion m/z, class, reaction, pathway along with a graphical view of the glycan and its possible theoretical fragments.
· SimGlycan highlights the m/z values which match those of theoretical fragments. Upon their selection, it plots, annotates, and exports an MS profile in .png format for your lab notebook. Using a simple interface, you can switch between Column and Scatter plots, zoom into specific plot regions, specify m/z range to display specific plot sections.
· SimGlycan enables you to assign your own rank to predicted structures, add comments and search fragments by their mass, name and m/z values.


Requirements:

· CPU: Pentium-III
· RAM: 256 MB
· Hard Disk Drive Space: 500 MB
· Screen Resolution: 800 x 600


Requirements:

· Fully demonstrates every function and feature of the product, but limited to the sample data provided.