SimGlycan Software

SimGlycan® Software

For research use only. Not for use in diagnostic procedures.

SimGlycan Software (a product of PREMIER Biosoft) predicts glycan and glycopeptide structures from SCIEX mass spectrometer-acquired MS/MS data, facilitating the identification of glycosylation sites and post-translational modifications. The software works directly with *.t2d and *.wiff files. Data generated from all SCIEX instruments can be processed using SimGlycan version 5.4 (and later), including the new support for the MIDAS™ Workflow. A perpetual license is included. Any upgrades of software features including database content are available at free of cost for the first year. Thereafter, for continued access to new upgrades of the product, this license will have to be renewed for each successive one-year term by paying an annual license fee to PREMIER Biosoft. This software is also available from the PREMIER Biosoft website

Overview

Key features:

  • Glycan/Glycopeptide MS/MS data analysis: Glycan/glycopeptide structures are identified by matching MS/MS data with theoretical fragmentation in the PREMIER Biosoft database using their proprietary search algorithm in batch mode.
  • Effective Scoring: SimGlycan creates a list of candidate structures by using precursor m/z and retention time* (optional parameter) as initial search predicate/s. Candidates are scored on the basis of the observed peaks that match their corresponding theoretical fragment ions. Candidate with the highest percentage of monosaccharide composition and fragmentation patterns explained by observed peaks in the spectrum is given maximum score. The score decreases for candidates with higher composition and fragmentation patterns left unexplained by the observed peaks.
  • Robust 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.
  • Create Glycan Templates*: Store glycan structures and other related information such as LC-retention times, column details, glycan class, biological sources, pathways, reaction, enzymes and links to other public databases. Users can add glycans into database by importing corresponding KEGG Chemical Function (KCF) format file. Adding multiple KCF files in batch is allowed.
  • Download MIDAS database*: A glycan template containing precisely curated glycan structures from MIDAS is available for download. You can import the template into the program as a custom database and restrict the glycan and glycopeptide search to this template only thereby removing false positives while analyzing these glycoproteins.
  • Easy workflow for glycopeptide MS/MS data analysis: Structural analysis of glycopeptides can be performed by specifying the sequence or mass of the attached peptide moiety. Options are provided to perform the search for a single peptide and multiple peptides in high throughput manner.
  • Direct Compatibility Analyst® Software: Experimental MS/MS data generated by all SCIEX mass spectrometers can be imported, enabling you to launch it directly from Analyst TF 1.6 and Analyst 1.6.2 Software using the companion software feature.
  • Draw and Compare: SimGlycan enables users to draw and edit glycan and glycopeptide structures and then compare the experimental with the theoretical data of the drawn structure.
  • Derivatized Glycans: Besides underivatized released-glycans, glycans treated with either permethylation or chemical derivatives used for reducing end-modifications can be analyzed. Glycans with custom reducing end modifications can be searched against the database just by specifying the delta mass of the modification.
  • LC-MS Data Processing: LC-MS and MS/MS data can be processed for peak detection, molecular feature identification and automated MS/MS data analysis. Glycans/glycopeptides identified from different LC-MS runs can be aligned on the basis of retention time facilitating comparative analysis.
  • Glycan quantitation*: SimGlycan facilitates relative quantitation of glycans based on intensity of custom and standard isobaric reporter ions.

*Available only in SimGlycan Enterprise Edition

Take advantage of the unique capabilities of SCIEX instruments: Because of its large mass range, high sensitivity, and soft desorption and ionization, MALDI time-of-flight (MALDI-TOF) mass spectrometry is widely used in the molecular weight determination of underivatized oligo- and polysaccharides. Traditionally, post source decay (PSD) has been used for structural analysis, and this can provide information related to sequence and branching; however, a lack of abundant cross-ring cleavages limits the linkage information that can be deduced from such experiments.

The MALDI TOF/TOF Systems are the only SCIEX instruments that combine high-energy MS/MS for cross-ring fragmentation for carbohydrate analysis (A and X- ions) with good precursor ion selection. This permits acquisition of more information on linkage position and points of branching, allowing the automated search routine in SimGlycanTM Software to correctly identify and characterize glycans without any secondary experiments.

QTRAP Systems are unique, hybrid triple quadrupole/linear ion trap instruments that delivers triple quadrupole scanning functions (e.g., precursor ion scans, MRMs) coupled with a high-sensitivity, ion-trap MS/MS and MS3 scan to enable sensitive and selective experiments for glycan and glycopeptide profiling. Because of the unique instrument configuration of the QTRAP System, the MS/MS spectra do not exhibit the low mass cut-off demonstrated by 3-D-ion traps. Subsequent MS3 fragmentation spectra can be obtained allowing mechanistic studies to be performed on the diagnostic fragments to confirm a predictive SimGlycan Software search result.

The QTRAP® 6500 system with 2000 m/z upper mass limit can sufficiently detect complex, hybrid and high mannose type containing glycans and glycopeptides. Expanded software functionality of Scheduled MRMTM Pro Algorithm enables quantitative glycopeptide profiling of therapeutic antibodies:

  • Group triggered MRM improves dwell and cycle time by only acquiring secondary transitions when primary transitions to the glycopeptides are above the set threshold. Therefore more glycopeptides can be screened.
  • Group triggered MIDASTM workflow triggers MS/MS only when multiple primary transitions for a glycopeptide are detected.

Increased efficiency of targeted detection for glycopeptides without enrichment strategies.