SimGlycanR
An Innovative MSn Data Analysis Tool
SimGlycanR predicts the structure of glycans and glycopeptides using mass spectrometry data. SimGlycanR accepts the experimental MS/MS data, matches them with its own database of theoretical fragments and generates a list of probable candidate structures. Each structure is scored to reflect how closely it matches your experimental data. Apart from the structural information, other biological information for the probable molecular structures such as the glycan class (N-Linked, O-Linked, heparin, lipopolysaccharide etc), reaction, pathway and enzyme are also made available for easy reference in case of structural elucidation of glycans while in the case of glycopeptide qualitative analysis, information such as Protein ID, Protein Name, Source, Classification, Class, peptide sequence, peptide mass etc are made available for identified glycopeptides.
Glycan & Glycopeptide MS/MS Data Analysis Tool
SimGlycanR is a comprehensive glycan and glycopeptide MS/MS data analysis tool with additional innovative module to validate an identified structure using Multi Stage/Sequential Mass Spectrometry (MSn). SimGlycanR generates a list of probable glycans or glycopeptides as per the selected module for data analysis and predicts the structure by calculating scores that reflect how closely the theoretical structures match the experimental MS profile saving you hours of laborious spectral interpretation works to assign accurate structures.
SimGlycanR includes comprehensive support for H, Li, Na, Mg and K adducts and adduct combinations such as Na + H, Li + H etc.
SimGlycanR provides comprehensive support to perform MSn data analysis which assists in resolving heterogeneity, branching patterns and isobaric oligosaccharide structures.
SimGlycanR can identify complex glycosaminoglycan structures even when modified with substituents such as sulfate, phosphate, ethanolamine etc. This functionality is useful for verifying the presence of carbohydrate residues modified with substituents.
SimGlycanR also includes comprehensive support for resolving glycopeptides obtained from a LC-MS/MS run of proteolytically digested purified glycoproteins. The Protein ID, Protein sequence or peptide sequences identified by a third party tool will be used as initial input in SimGlycanR in order to identify the glycopeptides from data dependent MS/MS data. SimGlycanR identifies probable glycan-peptide combinations and ranks them on the basis of observed peaks corresponding to diagnostic ions.
Glycan & Glycopeptide MS/MS Data Analysis for Studying Glycosylation
Protein Glycosylation, which is a key post-translational modification, is the result of addition of a glycan to a peptide sequence. Glycopeptides are known to exhibit multiple biological functions. In order to identify distinct functional properties for defined structural features, detailed information on the respective glycan moieties is essential. In order to understand all these phenomena, glycosylation analysis is an area of growing interest. Glycans have also been found to participate in many biological processes including embryonic development, inter and intracellular activities, coordination of immune functions, pathogens homing on their host tissues, cell division processes and protein regulations and interactions.
Glycoprotein glycosylation analysis has since long been a challenging task for biochemists. SimGlycanR assists in predicting the structure of a glycan from the released glycan MS/MS data or directly a glycopeptide (peptide chain modified with a single or two glycan structures) from glycopeptide MS/MS data acquired using various ionization techniques of mass spectrometry. Besides, it supports MS/MS data for released glycans with different chemical derivatives such as permethylation and various reducing terminal modifications. The facility to specify an user defined reducing end mass for permethylated glycans is also available. These profiles can be uploaded in SimGlycanR using standard file formats or directly from mass spectrometer raw file formats from AB SCIEX (TripleTOF™ 5600 System, TOF/TOF 5800, 4800 Plus MALDI TOF/TOF™ Analyzer, 4000 QTRAPR and QSTARR Elite Systems), Bruker Daltonics (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). All these features facilitate accurate study of protein glycosylation providing a strong base for developing a sensitive analytic approach to achieve complete quality analysis of glycoprotein therapeutics.
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