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SimGlycan Changelog

What's new in SimGlycan 5.95

Dec 24, 2021
  • 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.
  • Support for Windows 11: SimGlycan is now compatible with the new Windows 11 Operating System.
  • Fixes to reported issues.

New in SimGlycan 5.94 (Dec 3, 2020)

  • The new version includes:
  • 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.
  • 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.
  • 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.
  • Fixes to other reported issues.

New in SimGlycan 5.93 (Aug 5, 2019)

  • 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.
  • 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.
  • Fixes to reported problems.

New in SimGlycan 5.92 (Nov 1, 2018)

  • 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.
  • Fixes to reported issues.

New in SimGlycan 5.1 Build 510001 (Oct 10, 2014)

  • SimGlycan now allows exporting results including glycan/ glycopeptide structures into Microsoft excel file.
  • Structures can be exported with or without anomeric linkage information.
  • Fixes to the reported bugs.

New in SimGlycan 5.00 (Oct 10, 2014)

  • LC-MS and LC-MS/ MS high throughput data processing:
  • SimGlycan® now supports LC-MS and LC-MS/ MS high throughput data processing methods such as peak detection, smoothing, chromatogram deconvolution, peak alignment, peak deisotoping and adduct identification corresponding to the detected peaks. SimGlycan® can read LC-MS and MS/ MS raw data from .raw (Thermo Scientific™), .baf, .yep, .fid (Bruker Corporation), mzData and mzXML data files and generate peaklists for 100 raw data files (LC-MS runs) in a single run. SimGlycan® aligns detected peak m/z values to corresponding MS/MS spectra enabling seamless identification of glycan structures using precursors and product ions data from MS/MS data.
  • SimGlycan® also facilitates comparative and quantitative analysis of glycans identified from different biological samples. The peaks detected from different peaklists are aligned based on the agreement of retention time, m/z value, observed intensity and charge state using the RANSAC and LOESS techniques. Up to 100 peaklists can be aligned and the results can be exported to HTML, CSV and MS Excel formats.
  • Support for Agilent's Compound Exchange File (.cef):
  • SimGlycan® can read and import compounds with MS or MS/MS data along with the ion species information from Agilent's Compound Exchange File (.cef). You can import up to 100 CEF files in a batch mode.
  • Specify range:
  • You can specify a range of retention time, compound IDs and precursor m/z values to import spectra.
  • Data filters:
  • You can filter MS and MS/MS data based on specified m/z range and threshold intensity value.
  • Accurate assignment of ion species of MS/MS precursor ion:
  • SimGlycan® accurately assigns the ion species of MS/MS precursor m/z by probing its parent MS data. To match the MS/MS precursor m/z value against its parent MS data, you can specify either the m/z Precision (decimal points) or the Error Tolerance. By default, SimGlycan® considers assigned ion species for matching observed MS/MS precursor ion m/z value with the theoretical precursor ion m/z value, thereby precisely identifying glycan/glycopeptide structures.
  • Export search results to CEF files:
  • You can export and write glycan/glycopeptide search results to as many as 100 CEF files for further downstream processing in MassHunter and Mass Profiler Professional (MPP).
  • Improved fragment ion matching for adduct combinations:
  • SimGlycan® now considers all adduct ion combinations dominantly observed on the MS/MS spectra for fragment ion matching. For example, if the chosen adduct combination is M + 2Na + 1H, SimGlycan® considers M + Na, M + 2Na, M+H for fragment ion matching, in addition to M + 2Na + 1H.
  • Export Annotated Peaklist:
  • You can export annotated peaklist for all search results from 20,000 MS/MS spectra.
  • Ammonium Adduct Support:
  • You can analyze MS/MS data ionized with ammonium adduct (NH4+) and its combination with the already supported adducts, viz H, Li, Na, K, Mg2+ and HCOO-.

New in SimGlycan 4.5 (Oct 10, 2014)

  • Enhanced Project Management:
  • You can now import 20,000 spectra in a project. This is a considerable improvement over the last version where 1500 spectra could be loaded.
  • Users of Thermo Scientific™ instruments can specify a range of retention time, scan number and precursor m/z values to import spectra.
  • Increased Throughput for MS/MS Search:
  • You can now analyze 1000 spectra in a batch run, doubling the data handling capability from the previous versions.
  • Monoisotopic Mass Identification for Precursor m/z Values:
  • SimGlycan now checks if the precursor m/z of an MS/MS and MSn spectra is the monoisotopic mass of an isotope cluster. If the precursor m/z values for MS/MS and higher level MSn correspond to a monoisotopic peak the corrected precursor m/z values are imported.
  • New Adduct:
  • SimGlycan now supports the Formate adduct (HCOO) and its combination with the already supported adducts, viz H, Li, Na, K and Mg.
  • Improved Confidence:
  • Users can now reduce the reporting of false positives by setting the following
  • Threshold level for percentage of glycosidic bonds evident from the MS/MS spectra as a predicate for candidate structures.
  • Specify the fragment ion series observed in the MS/MS spectra based on instrument settings and ionization technique to eliminate false positives.
  • Comprehensive Project Report:
  • The following functionality enable users to organize the results of the data analysis:
  • You can now include search results from 20,000 MS/MS spectra in a single report
  • Specify what information you would like to see
  • Filter the search results based on percentage match, proximity score, precursor ion intensity
  • Sort the search results based on precursor m/z, precursor intensity, retention time and MS Level in both, ascending and descending order
  • Filter out MS/MS spectra with no search results
  • Include separators to distinguish results from different samples
  • Save options specified for generating a report as a template for repeat use.
  • Relative Quantification:
  • Relative quantification of identified glycans or glycopeptides is now possible by normalizing the observed precursor intensity values based on the intensity of an internal standard. You can also export information such as the intensity of the internal standard; normalized intensity and the relative quantity to the project report.

New in SimGlycan 4.02 (Oct 10, 2014)

  • Improved Speed:
  • The new version offers compatibility with 64-bit Windows OS affording significant enhancements in processing large data.
  • Improved Analysis:
  • The ranking algorithm is further improved to accurately account for the charge state assigned to product ions, resulting in better matched results.
  • Filter Criteria:
  • The "Biological Source" of the protein can now be set to filter out unwanted results.

New in SimGlycan 4.01 (Oct 10, 2014)

  • Import "label data" from native data files of Thermo Scientific™ acquired by FTMS analyzer (*.raw).
  • Import data from *.raw file for a specified retention time range.
  • Display information such as base peak intensity, total ion current and type of analyzer while loading data in a project.

New in SimGlycan 4.00 (Oct 10, 2014)

  • Increased Glycan Support:
  • SimGlycan® database is updated to include 12,897 additional glycans, taking the total database strength to 22,456. The database includes glycans from bacterial taxa, additional glycosaminoglycans, chinese herbs etc.
  • High Resolution Data Support:
  • MS/MS and MSn data analysis can now be performed for high resolution data with an error tolerance of up to 1 parts per million (ppm) or 0.1 milli dalton (mDa).
  • Mg Adduct Support:
  • SimGlycan® now includes support for Mg adduct in addition to the previously supported H, Li, Na and K adducts and their combinations.
  • Missed Cleavage Combination Support:
  • Now multiple missed cleavages can be specified (e.g., 0 and 1, 1 and 2 etc.) for generating peptides.
  • The exported report now includes the search parameters used during the analysis, enabling it to be used for further analysis or referencing data.

New in SimGlycan 3.50 (Oct 10, 2014)

  • SimGlycan® now includes comprehensive support for Li and K adducts and adduct combinations such as Na+H, Li+H etc., in addition to the previously supported H and Na adducts.
  • The new version includes an enhanced ranking mechanism where proximity score is calculated based on the composition score and the branching score. The score also factors in the extent to which the peaks match with important diagnostic ions, improving SimGlycan's ability to predict the correct structure.
  • SimGlycan now displays the chemical formula of the glycan in addition to its structure and composition.
  • Users now have the option to filter our low intensity peaks or noise from the peak list data.

New in SimGlycan 3.00 (Oct 10, 2014)

  • Glycopeptide Qualitative Analysis: SimGlycan® now includes comprehensive support to identify glycopeptides of complex glycoprotein mixtures separated by LC and detected by MS/MS. The protein ID, sequence or peptide sequences identified by using third party tools is used by SimGlycan® to identify probable glycan-peptide combinations. SimGlycan ranks them on the basis of the peaks observed in the MS/MS data that correspond with diagnostic ions.
  • Seamless integration with Thermo Scientific™ mass spectrometers will now enable SimGlycan® to load native files, without the use of third party conversion tools. SimGlycan® is compatible with the following Thermo Scientific™ mass spectrometers: LTQ FT Ultra, LTQ Velos, LTQ XL, LTQ Orbitrap Discovery, LTQ Orbitrap Velos, LTQ Orbitrap XL, MALDI LTQ Orbitrap.
  • In addition, users can now plot all types of glycosidic fragments at the same time while annotating the spectra in symbolic representation format.
  • For permethylated glycans, it is now possible to specify user defined reducing end mass.

New in SimGlycan 2.92 (Oct 10, 2014)

  • SimGlycan® now 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 increases, generated fragments become structure specific, assisting in resolving isobaric oligosaccharides and following fragmentation pathways.
  • Seamless integration with Waters mass spectrometers will now enable opening the lcs files directly in SimGlycan®, without the use of third party conversion tools. SimGlycan® is compatible with the following Waters mass spectrometers: SYNAPT G2 HDMS, SYNAPT G2 MS, Xevo G2 QTof, Xevo QTof MS, Xevo TQ MS and Xevo TQ-S platforms.

New in SimGlycan 2.91 (Oct 10, 2014)

  • SimGlycan now includes support for AB SCIEX TripleTOF™ 5600, updates to the glycan database and fixes to reported problems.

New in SimGlycan 2.90 (Oct 10, 2014)

  • Rapid advancement in mass spectrometry has enabled high throughput experimentation for glycan identification. Keeping pace with such advancements, SimGlycan® can now analyze LC-tandem MS runs containing hundreds of scans in a batch. Users can load up to 1500 profiles in a project and analyze 500 in a single search run. A template for search parameters can be created to be applied to all data sets.
  • SimGlycan® can now identify complex glycosaminoglycan structures even when modified with substituents such as sulfate, phosphate, ethanolamine, etc. The spectra is annotated with subsequent loss of substituents from their corresponding glycosidic fragments. This functionality is most useful for verifying the presence of carbohydrate residues modified with substituents.
  • The built-in drawing canvas also provides the facility to modify a glycan structure drawn on the canvas not only with carbohydrate residues and linkage positions but also with different substituents that might have modified the carbohydrate residues. This enhancement makes identifying modified glycan structures heuristically much more robust.
  • The SimGlycan® database is now updated with over a thousand new glycans to provide more accurate search results.

New in SimGlycan 2.75 Build 264005 (May 25, 2009)

  • SimGlycan now includes comprehensive support for resolving glycopeptides. You can now analyze the intact structure of a completely unknown glycopeptide. SimGlycan searches for all the possible glycan-peptide combinations and displays the percentage match between the theoretical and experimental data. This helps in understanding the degree of proximity between the probable glycopeptide structure and the experimental MS profile.
  • Apart from displaying the percentage match for peptide and glycan/peptide fragments, SimGlycan also highlights all the matched and unmatched fragments, making it easier to determine the probable structure.