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SimGlycan®

Posters

Title & Abstract Author & Venue

Automated and Rapid Characterization of Low-Molecular-Weight Heparin Oligosaccharides Using TripleTOF 5600 Mass Spectrometer with SimGlycan Software

Low molecular weight heparins (LWMH) - Enoxaparin, Parnaparin, Certoparin, Deltaparin, Tinzaparin, etc. - have been reported to be the key drugs and are as safe and effective as Unfractionated Heparin (UFH) [1,4] which further necessitates in-depth study of new regulatory drugs. Despite its medical and biological importance, LWMHs are relatively uncharacterized in terms of its chemical structures due to its structural complexity. Liquid Chromatography coupled with Mass Spectrometry workflows have been increasingly used for potential high throughput identifications of the LMWH oligosaccharides.

Meitei, N.S., Pujari, R., Apte, A., Uppal, A.

65th ASMS Conference on Mass Spectrometry and Allied Topics (2017), Indianapolis, IN

SimGlycan®: Informatics Support for Automated Characterization of Low-Molecular-Weight Heparin Oligosaccharides Using MS2 Data from TripleTOF® 5600 Mass Spectrometer

Recent reports suggested that patent protection worth of $80 billion for several biosimilars, including Low molecular weight heparins (LWMH) - Enoxaparin, Parnaparin, Certoparin, Deltaparin, Tinzaparin, etc. - has been expired and abbreviated new drug applications have been approved by different regulatory bodies, namely, the Food and Drug Administration (FDA), USA; Central Drugs Standard Control Organization (CDSCO), India, etc.

Meitei, N.S., Pujari, R., Apte, A., Uppal, A.

Applied Pharmaceutical Analysis (2017), Organized by The Boston Society, Ahmedabad, India

Speeding up the High Throughput Searches for Glycan Analysis

A typical LC-MS glycomic data processing includes peak detection, deconvolution of peaks of co-eluting isomers, molecular feature extraction, and selection of correct precursor m/z values from the isotope cluster for MS/MS data analysis.

Meitei, N.S., Apte, A., Goswami, R., Saba, J.

64th ASMS Conference on Mass Spectrometry and Allied Topics (2016), San Antonio, Texas

Development of Bioinformatics support for Quantitative Glycomics using Tandem Mass Tags

AminoxyTMT reagents enable relative quantitation of glycans in a MS/MS spectrum. However, there are no bioinformatics tools to automate the qualitative/ quantitative analysis.

Meitei, N.S., Apte, A., Snovida, S., Saba, J., Rogers, J.

14th Human Proteome Organization World Congress (2015), Vancouver

Profiling the Distribution of N-Glycosylation in Therapeutic Antibodies using the QTRAP® 6500 System

Immunoglobulin G molecules have become attractive as targeted therapeutic proteins, due to their high specificity and long circulation time. Glycosylation patterns determine the stability and bio-disposition of these recombinant protein drugs in vivo, as well as the efficacy, folding, binding affinity, specificity and pharmacokinetic properties.

Albanese, J., Hunter, C.L., Meitei, N.S.

14th Human Proteome Organization World Congress (2015), Vancouver

SimGlycan: Informatics tool for creating glycan templates to enable high throughput glycan identification from Liquid Chromatogram - tandem mass spectrometry data

Protein glycosylation is one of the well-known post-translational modifications, and in biological processes in living organisms it plays an important role. Monitoring changes in the amount and structure of sugar chains makes it possible to monitor sugar chain modification of proteins and various diseases.

Meitei, N.S., Apte, A., Goswami, R., Chatterjee, M.K., Park, J.

34th Annual Conference of The Japanese Society of Carbohydrate Research (2015), Tokyo

Development of Bioinformatics Support for High Throughput Isomeric Separation and the Structural Identification of Glycans by LC-MS

The separation of glycans by chromatography prior to MS analysis can reduce sample complexity, minimize ion suppression, and increase dynamic range and separation of structural isomers.

Meitei, N.S., Apte, A., Aich, U., Saba, J.

63rd ASMS Conference on Mass Spectrometry & Allied Topics (2015), St. Louis

Informatics Support for Isomeric Separation and the Structural Identification of Labeled N-Glycans from Proteins

Develop a software to facilitate LC-MS and MS/MS glycan data that have been acquired for separation and identification of various complex N-linked glycans from proteins using a novel high resolution mixed-mode column and an Orbitrap Fusion Tribrid mass spectrometer.

Meitei, N.S., Apte, A., Aich, U., Saba, J.

13th Human Proteome Organization World Congress (2014), Madrid

Automating Mass Spectrometry-Based Quantitative Glycomics using Tandem Mass Tag (TMT) Reagents with SimGlycan

One of the emerging trends in glycomics research is the innovation related to accurate MS based quantitative analysis of glycans1-4. Recently, we have introduced aminoxyTMT Reagents, which enable efficient relative quantitation of carbohydrates, improved labeled-glycan ionization efficiency and increased analytical throughput.

Meitei, N.S., Apte, A., Snovida, S., Saba, J., Rogers, J.

62nd ASMS Conference on Mass Spectrometry and Allied Topics (2014), Baltimore

Automated Glycan Structural Isomer Differentiation Using Bioinformatics Tool

Mass spectrometry (MS) has emerged as a powerful tool for the structural elucidation of glycans. The use of permethylation in combination with multistage fragmentation (MSn) is a critical step in glycan structural characterization.

Saba, J., Apte, A., Meitei, N.S., Viner, R.

59th ASMS Conference on Mass Spectrometry and Allied Topics (2011), Denver

Integration of SimGlycan into Waters Glycan/Glycopeptide Analysis Workflow

Translating New Technologies in Improved Workflows for Biotherapeutic Analysis.

Berger, S.J.

58th ASMS Conference on Mass Spectrometry and Allied Topics (2010), Salt Lake City

Application Notes

Title & Abstract Author & Publication

A Unique Workflow for Glycoprotein Characterization from Sample Preparation to MS/MS Spectral Interpretation

Protein glycosylation is a complex dynamic post-translational modification, which is used by an organism to regulate a number of important protein function.

Albanese, J., Lee, R. (2011)
J Biomol Tech., 22(Suppl), S57

SimGlycan™ Software*: A New Predictive Carbohydrate Analysis Tool for MS/MS Data Automated Data Interpretation for Glycan Characterization

The analysis of carbohydrates is of great importance in modern biochemistry and is often tackled using various analytical techniques, including mass spectrometry.

Albanese, J., Glueckmann M., Lenz C. (2010)

Novel Glycan Column Technology for the LC-MS Analysis of Labeled and Native N-Glycans Released from Proteins and Antibodies

Because glycosylation is critical to the efficacy of antibody therapeutics, the FDA requires that a consistent human-type glycosylation be maintained for recombinant monoclonal antibodies (mAb), irrespective of the system in which they are produced.

Aich, U., Birznieks, I., Saba, J., Liu, X., Viner, R., Hao, Z., Gendeh, G.S., Rao, S., Huhmer, A., Agroskin, Y., Pohl, C. (2013)
* Indicates mandatory



An Innovative Glycan and Glycopeptide MSn Data Analysis Tool SimGlycan® predicts the structure of glycans and glycopeptides using mass spectrometry data.

SimGlycan® accepts the experimental MS/MS and Multi Stage/Sequential mass spectrometry (MSn, n>2) 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 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.

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  • Robust Glycan and Glycopeptide Database
  • Support for MALDI MS/MS and LC-MS/MS Workflows
  • Data Input File Formats
  • Accurate Ranking Mechanism
  • Additional Filters For Precise Results
  • Comprehensive Result Analysis
  • LC-MS and LC- MS/MS Data Processing
  • High Throughput Analysis
  • TMT Quantitation
  • Multi Stage Mass Spectrometry (MSn) Data Analysis
  • Glycopeptide Qualitative Analysis
  • Project Management
  • Draw Glycans
  • Mass Spectra Interpretation

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