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SimGlycan® Upgrades

SimGlycan version 5.95 Released

The new version includes:

  1. Improved Shimadzu Native File Support: SimGlycan now accommodates the latest data reading algorithm offered by Shimadzu Corporation for seamless integration and accurate analysis. This change significantly improves the software’s capability in reading Shimadzu's native data file (.lcd), which further helps in more accurate peaklist generation and increases the accuracy of the high throughput glycan identification.

  2. Support for Windows 11: SimGlycan is now compatible with the new Windows 11 Operating System.
  3. Fixes to reported issues.

SimGlycan version 5.94 Released

The new version includes:

  1. Improved Raw Data Loading: SimGlycan now accommodates improved raw data loading mechanism to ensure correct charge state assignment for MS/MS scans. This facilitates accurate analysis of data acquired using direct infusion workflow.

  2. Improved LC-MS Algorithm: With an improved algorithm, SimGlycan now can generate more accurate LC-MS peaklists from the raw data files. An option is now available to detect compounds within the charge state range specified.
  3. Improved Loading of Shimadzu (QTOF) Native Data Files: SimGlycan now accommodates the latest data reading algorithm offered by Shimadzu Corporation. This has significantly improved the data loading capability of the software for the Shimadzu QTOF instrument series.
  4. Fixes to other reported issues.

SimGlycan version 5.93 Released

The new version includes:

  1. More Accurate LC-MS Peak Detection & Picking: SimGlycan now adopts a more efficient and faster peak picking algorithm with effecient data handling. It enables users to define a charge state range and a minimum number of isotopologues in an isotopic cluster for a valid LC compound.

  2. Addition of Infliximab Glycans to the SimGlycan Database: Unique Infliximab N-Glycan structures are curated and added to the SimGlycan database enabling mass spectrometry based therapeutic glycan analysis. Infliximab is a chimerical immunoglobulin, which is responsible for the generation of immunogenicity against autoimmune diseases.
  3. Fixes to reported problems.

SimGlycan version 5.92 Released

The new version includes:

  1. Faster LC-MS Peak Picking: With a new improved peak picking algorithm and faster data handling, SimGlycan is now able to process LC-MS/MS data faster and with more efficient and accurate peak picking.

  2. Fixes to reported issues.

SimGlycan version 5.91 Released

The new version includes:

  1. Improved Data Reading and Peak Picking Algorithm for Experimental Data Files: SimGlycan now offers improved and more accurate assignment of precursor m/z values of MS/MS scans while loading the experimental data file. This algorithm identifies the isotope cluster from MS 1 data and assign m/z of the monoisotopic peak as the precursor m/z of the MS/MS scans. This further enables correct charge state assignment for the MS/MS scans as well. This improvement is available for the following data files:

    • .raw (DDA) from Waters Corporation

    • .lcd (QTOF) from Shimadzu Corporation

  2. Analysis Support for Shimadzu's QTOF Data: SimGlycan now supports analysis of  QTOF data generated by Shimadzu Corporation LCMS-9030 Quadrupole Time of Flight (QTOF) mass spectrometry (MS) system. The software allows direct loading of their native .lcd file format for glycan identification and further downstream analyses.

  3. Improved High Throughput Search: Time required for high throughput search and loading of identified glycans/ glycopeptides has been significantly reduced enabling you to complete your analysis faster.

  4. Fixes to previously reported issues.

SimGlycan version 5.90 Released

The new version includes the following:

  1. Improved LC-MS Peak Picking Algorithm: An efficient algorithm for detecting LC peaks, and subsequent molecular feature finding from the raw data is now implemented. The improvized algorithm accurately detects LC-compounds along with their isotope envelopes enabling the program to accurately assign precursor m/z values, and their correct charge states for MS/MS scans.

  2. LC-MS Peak Detection and Molecular Feature Finding for Preferred Masslist: You can submit a preferred masslist for peak detection and picking. This functionality significantly reduces the likelihood of LC-peaks not detected for low abundant compounds in complex biological samples.

  3. Support for DRAG Analysis: Dual Reactions for Analytical Glycomics (DRAG ) is a recently reported stable isotope labeling approach for quantifying both neutral and sialylated glycans. The new version of SimGlycan offers an optimized LC peak picking template for researchers working with Orbitrap LC-MS based workflows.

  4. Faster Database Search: The latest version of the program is up to 5 times faster as compared to the previous versions.

  5. Fixes to the previously reported issues.

SimGlycan version 5.80 Released

The new version includes the following:

Improved Peak Picking Algorithm for Reading Data from Thermo Fisher Scientific Files: SimGlycan now offers improved and more accurate assignment of precursor m/z values of MS/MS scans while loading Thermo Fisher Scientific native .raw files by identifying isotope clusters from MS 1 data. The identified isotope clusters can be exported to a shareable report in Microsoft Excel.

SimGlycan version 5.70 Released

The new version includes the following:

  1. Multiple Biological Source Selection: SimGlycan now enables you to select multiple biological sources while performing MS/MS search in the SimGlycan master database. You can select up to 20 specific sources to have the software report the glycans of interest.

  2. Multiple Databases Selection: The latest version of SimGlycan supports selection of multiple target databases for performing a glycan search. The software reports candidate glycan structures from the selected databases and displays the name of the source databases as well. **

  3. Faster loading of Thermo Fisher Scientific native .raw files using the recently released RawDataReader from the company.

  4. Fixes to the previously reported issues.

** Functionality available in SimGlycan Enterprise Edition

SimGlycan version 5.61 Released

The new version includes the following:

  1. Addition of New Glycans in SimGlycan Master Database: The SimGlycan master database is updated with curated (a) N-glycans derived from Monoclonal antibody (mAb), Bovine Fetuin, Chinese Hamster Ovary (CHO), (b) glycosaminoglycans derived from Low Molecular Weight Heparin (LMWH), and (c) polysaccharides derived from plants. Following are brief descriptions of the glycans and their sources:

    • N-Glycans of Monoclonal Antibody (mAb): Recombinant monoclonal antibody therapeutics (mAbs) represent the largest group of therapeutic proteins as a major new class of drug. SimGlycan database now includes 71 curated unique N-Glycan structures of mAb which play critical role in immunity, pathogenicity and other cellular processes.

    • N-Glycans of Chinese Hamster Ovary (CHO): Therapeutic proteins obtained from Chinese Hamster Ovary (CHO) cell lines show almost same glycosylation pattern as human, and hence, are most widely used in the development of biosimilar products. Now, we have added 130 curated unique N-Glycan structures into SimGlycan database.

    • N-Glycans of Bovine Fetuin: Fetuin (blood proteins) is an important component of bone metabolism regulation, insulin resistance, protease activity control etc. It has also been identified as a biomarker for neurodegenerative disease. We have now added 71 unique N-Glycan structures from Bovine fetuin, that play a critical role in these processes.

    • Polysaccharides of Plants: Plant polysaccharides' unique characteristics of the water-soluble colloids makes food highly nutritious and hence, has high value in food industry. 210 unique polysaccharides have been added into the SimGlycan database.

    • Low Molecular Weight Heparin (LMWH): Low Molecular Weight Heparins are coagulation inhibiting glycosaminoglycans. Because of the anti-coagulation nature, these glycosaminoglycans are therapeutically engineered to prevent thrombosis, and thus has high medicinal value. 317 glycosaminoglycans of LMWH have been added into the SimGlycan database.

      These structures were curated from the published papers in journals namely Analytical chemistry, Biochemistry, Carbohydrate Research, European Journal of Biochemistry, Food Hydrocolloids, Journal of Biological Chemistry, Journal of Chromatography, and Phytochemistry.

  2. Fixes to reported issues.

SimGlycan version 5.60 Released

The new version includes the following:

  • Exclude Monosaccharide(s) Filter: SimGlycan can now filter glycan structures based on monosaccharide residues:

    1. SimGlycan Server
    Using the web-panel, you can search glycan structures which do not contain specific monosaccharide residues. **

    2. SimGlycan Client
    You can specify one or multiple monosaccharide residue(s) in the exclusion list while performing a glycan search. The program will not report glycan structures which contain any of the excluded monosaccharide residues in the result. This functionality helps eliminate false positives.

  • Curate Glycan Structures: SimGlycan's intuitive web-panel now enables you to curate glycans from the master database based on their biological sources. **

  • Fixes to the reported issues

** Available in SimGlycan Enterprise Edition only

SimGlycan version 5.50 Released

The new version includes the following:

  • Identification of Glycans Labeled with Dual Modifications Strategies and Stable-isotope labeling techniques: SimGlycan now supports identification of glycans labeled using

    1. Dual Modifications Strategies
    - reducing end modified with a fluorophore e.g., 2-AA
    - modification of the fluorophore e.g., methylamidation
    - modifications of target carbohydrate residues e.g., labeling of sialic acids with methylamidation, or 1,2-diamino-4,5-methylenedioxybenzene (DMB)

    This functionality provides the first ever software solution, to the best of our knowledge, for Sialoglycomics.

    2. Stable-isotope Labeling
    The software can identify glycans using MS/MS data of samples treated with stable isotopic labeling techniques. You can now compare isotopically distinct forms of the same glycan structure originating from different biological samples such as control and diseased.

  • Loading of Raw Data (DDA Method) Directly from Waters .raw File Format: SimGlycan can now read DDA data directly from Waters .raw format files. This functionality is in addition to the peaklist support from Waters .lcs format files.

  • Identification of Glycans Labeled with RapiFluor-MS Reagent: SimGlycan now facilitates structural analysis of glycoforms labeled with GlycoWorks RapiFluor-MS reagent (Waters Corporation), derived from complex mixtures.

  • Fixes to the reported issues.
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