PREMIER Biosoft logo  


Download Flyer
SimGlycan, an Innovative MSn Data Analysis Tool
Home >> Products >> SimGlycan® >> Features
PREMIER Biosoft Facebook link PREMIER Biosoft Twitter link
SimGlycan®

Features

Robust Glycan and Glycopeptide Database

SimGlycan® database is a large relational database containing 22,456 glycans, 22814 glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.

Accurate Ranking Mechanism

All possible glycan/glycopeptide structures are ranked and scored based on our proprietary search and score mechanism. The ranking mechanism is based on calculating the proximity score, which is a numerical representation of how closely the experimental properties (composition and branching pattern) of the glycan/glycopeptide match with those of the glycans/glycopeptides in the database.

Comprehensive Result Analysis

For every probable glycan or glycopeptide structure, SimGlycan® provides in-silico fragments, structure, sequence, composition, chemical formula, molecular mass, class, reaction, pathway, enzyme and other database links (CarbBank, Glycome db, JCGGDB).

SimGlycan® accepts peaklist data (experimental m/z and intensity values) of both released glycans and glycopeptides as input. 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. SimGlycan® allows direct automatic loading of input data files generated by mass spectrometers from AB SCIEX (TripleTOF™ 5600 System, TOF/TOF 5800, 4800 Plus MALDI TOF/TOF™ Analyzer, 4000 QTRAP® and QSTAR® Elite Systems), Bruker Corporation (ultrafleXtreme™ MALDI TOF/TOF, ultraflex™ MALDI TOF/TOF, autoflex™ TOF and TOF/TOF, maXis™ UHR-TOF, micrOTOF™, micrOTOF-Q™, solariX™ Qq-FTMS, and amaZon™ ion trap series), Thermo Scientific™ (LTQ FT Ultra, LTQ Velos, LTQ XL, LTQ Orbitrap Discovery, LTQ Orbitrap Velos, LTQ Orbitrap XL, MALDI LTQ Orbitrap, Orbitrap Elite and Q Exactive) and Waters (SYNAPT G2 HDMS, SYNAPT G2 MS, Xevo G2 QTof, Xevo QTof MS, Xevo TQ MS and Xevo TQ-S platforms). Other mass spectrometers are supported using mzData and mzXML. Besides, manual entry, TXT and XLS file formats are also accepted by SimGlycan®. No matter what make your instrument is, the output can be converted to these formats using third party tools.

High Throughput Analysis

Rapid advancement in mass spectrometry enables high throughput experimentation for glycan identification. To keep pace with such advancements, SimGlycan® can analyze LC-tandem MS runs containing hundreds of scans in batch mode. Furthermore, users can create and use search parameter templates that can be applied to all data sets. Users can perform glycan/glycopeptide search for high resolution accurate mass (HRAM) data with an error tolerance up to 20 parts per million (ppm) or 2000 milli Dalton (mDa).

Multi Stage Mass Spectrometry (MSn) Data Analysis

SimGlycan® includes comprehensive support to perform Multi Stage/Sequential Mass Spectrometry (MSn) data analysis. MSn, a technique wherein the product ions from MS/MS (or previous stage MS) are subjected to re-fragmentation, is one of the most effective techniques in resolving heterogeneity, branching pattern and isobaric oligosaccharide structures. It allows discrimination of glycans having similar characteristic fragment patterns which are otherwise indistinguishable in MS/MS spectra. As the level of MS (n) increases, generated fragments become structure specific which assists in resolving isobaric oligosaccharides or detailed characterization of selected structures.

Glycopeptide Qualitative Analysis

Many of the mass spectrometers allows the capture of MS/MS data as compounds elute from in line separation systems. Such LC-MS/MS approaches generate extremely large datasets, requiring sophisticated informatics tool to assign glycopeptide structures over a complete chromatographic separation. This would enhance analytic productivity and provide greater depth of analysis of mass spectrometric glycoproteomic data. SimGlycan® now includes comprehensive support for identifying glycopeptides of complex mixtures separated by LC and detected by MS/MS in batch processing mode. The Protein ID, Protein sequence or Peptide sequences identified by using a third party tool will be used by SimGlycan® as initial input. SimGlycan® identifies probable glycan-peptide combinations and ranks them on the basis of observed peaks in the MS/MS data corresponding to diagnostic ions from theoretical glycopeptide. High resolution accurate mass data with an error tolerance between 1 to 20 parts per million (ppm) and 0.1 to 2000 milli Dalton (mDa) can be analyzed.

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 load up to 1500 MS profiles datasets. 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 glycan analysis projects.

You can access glycan related information at the click of a button. Unlike web based applications, SimGlycan® saves it on your own computer. The available information consists of:

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.

i) Glycosidic Fragments: Single glycosidic and glycosidic/glycosidic fragments are displayed.

ii) Cross Ring Fragments: Single cross ring and glycosidic/cross ring fragments are displayed.

Glycopeptide Structure: Displays the peptide sequence and the sites of protein glycosylation along with the glycan structures.

Annotate Mass Spectra and Generate Reports

SimGlycan® can annotate mass spectra using cartoons or Domon-Costello nomenclature. The charge state of the fragment is also depicted. Read more...

Draw Glycans

SimGlycan® enables users to draw and edit glycan and glycopeptide structures. A monosaccharide, peptide chain or a substituent such as HSO3, Etn can be added or deleted and branching points and anomeric linkages can be modified at the click of a button. At each step, the fragmentation of the drawn structure enables a user to compare the experimental and theoretical data, enabling the user to see whether his modification brings the theoretical glycan closer to the experimental data. This feature greatly assists in resolving glycan structures, especially when data for glycans of interest is not yet available.

draw glycan, sulphonated glycan

Mass Spectra Interpretation

SimGlycan® helps in interpreting a mass spectra by highlighting the experimental m/z values that match those of theoretical fragments and generates an annotated spectrum depicting the loss of consecutive monosaccharide units. This helps researcher to establish the branching pattern and verifying the basic unit of glycan. Each peak can be represented using cartoons or Domon Costello nomenclature. Charge states of fragments are also displayed if the fragments are multiply charged.

SimGlycan® enables generating an annotated mass spectra either to fit on a page or based on the area of interest. It also exports it for sharing the findings with your colleagues. The simple interface enables you to zoom into specific plot locations, specify m/z range to display specific plot sections and also to export plots as image files to MS PowerPoint, for publishing results and sharing information with colleagues.

Cartoons are constructed using standard Consortium for Functional Glycomics (CFG) nomenclature for monosaccharides (custom symbols are used where CFG annotations are not available). You can simultaneously plot all types of glycosidic fragments while annotating the spectra in symbolic representation format.

Copyright ©1994- PREMIER Biosoft. All rights reserved.