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Upgrades

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SimGlycan® version 5.43 Released

The upgrade accommodates fixes to reported issues.

SimGlycan® version 5.42 Released

The new version includes the following enhancements:
SimGlycan has now incorporated an improved peak picking and peak detection algorithm allowing faster processing of LC-MS and MS/MS data. The new proprietary algorithm enables the program to perform peak detection and molecular feature finding for any raw data file at least 3 times faster than the previous versions of the program while ensuring important compounds and their molecular features are not missed out.

SimGlycan® version 5.41 Released

The new version includes the following:

• Faster algorithm for LC-MS peak picking and peak detection
• Improved user interface
• Fixes to reported issues

SimGlycan® version 5.40 Released

The new version includes the following:

• The Project Management panel now highlights the scans for which the analysis was completed, giving a quick visual cue for locating the search results. The color of the highlight indicates the nature of the search performed. For example, scans in blue indicate successful glycan searches, green indicates glycans with known peptides and red, a search with no results.
  
  
• A new improved and more accurate search algorithm.
  
  
• Fixes to reported issues.

SimGlycan® version 5.30 Released

The new version includes the following:

• Support for mzML (1.1.0) data format.
  
  
• Enhanced functionality for annotating glycan and glycopeptide fragments in mass spectra. Structures can be edited, you can choose one or multiple structures for editing at a time. Selection over the spectra can be zoomed into so as to study and highlight important areas. Structures can be moved or reordered for comparing peaks or isobars.
  
  
• Fixes to reported issues.

SimGlycan® version 5.20 Released

The new version includes the following enhancements:

• Enhanced file loading capacity: SimGlycan can now accommodate 500,000 spectra in a single project, making it much more convenient to work with larger datasets.
  
  
• New improved high throughput search: Time required for high throughput search and loading of identified glycans/ glycopeptides has been significantly enhanced enabling you to complete your analysis faster.
  
  
• Faster loading of AB SCIEX files: AB SCIEX's WIFF file loading is now much faster than ever before. SimGlycan 5.20 has redesigned the WIFF import mechanism, eliminating the need of using Analyst® which was previously required for loading of files.
  
  
• Fixes to reported issues.

SimGlycan® version 5.10 Released

The new version includes the following enhancements:

• 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 reported bugs.

SimGlycan® version 5.00 Released

The new version includes the following enhancements: 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^-.

SimGlycan® version 4.5 Released

It new version includes the following enhancements: 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.

SimGlycan® version 4.02 Released

The new version now has: 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.

SimGlycan® 4.01 Released

The new version SimGlycan® version 4.01 enables users to:

• 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.

SimGlycan® 4.00 Released

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. Note: Due to database updates, analysis results may vary from the previously obtained results.

SimGlycan® 3.50 Released

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.

SimGlycan® 3.00 Released

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.

SimGlycan® 2.92 Released

1) 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. 2) 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.

SimGlycan® 2.91 Released

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

SimGlycan® 2.90 Released

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.

SimGlycan® 2.75 Released

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.

SimGlycan® 2.71 Released

SimGlycan now includes improved support for all the scan types from ABI mass spectrometers in addition to a host of improvements to the search and score algorithm, the glycan database, user interface and fixes to reported problems.

SimGlycan® 2.70 Released

SimGlycan® has now the ability to annotate mass spectra showing:

• Cartoons of glycan or peptide fragments. Charge states of fragments are also displayed if the fragments are multiply charged.
• Domon-Costello fragment names for glycans and standard peptide fragments names along with the corresponding charge states (if multiply charged).

SimGlycan® now includes the ability to draw and edit glycan as well as glycopeptide structures. At each step, the fragmentation of the drawn structure enables a user to compare the experimental and theoretical data, and thus to see whether his modification brings the theoretical glycan closer to the experimental data. This methodology facilitates in identifying a novel glycan structure irrespective of the glycan mass and improves the ability to come as close as possible to the unknown glycan structure. SimGlycan® now includes a considerably enhanced ranking algorithm that is equipped to handle multi-charged product ion and fragment ion data. If the input peaklist is multiply charged, user now has the flexibility to predict glycans by comparing the product ions against the theoretical data at different charge states.

SimGlycan® 2.60 Released

SimGlycan® has an improved sequence view. The consecutive loss of monosaccharide units with respect to a reference peak say Precursor ion m/z can now be depicted. This feature is not available in any other product, to the best of our knowledge. Furthermore, loss of branches (if any) are also depicted. This feature is especially useful since it allows users to establish the branching pattern of a glycan as well as verifying the basic units of the glycan by analyzing the spectrum. The attractively annotated spectra helps in publishing results and sharing information with colleagues. Raw file formats generated by mass spectrometers from Bruker Corporation mass spectrometers (APEX, micrOTOF, micrOTOF-Q and esquire series) can now be seamlessly opened in SimGlycan®. The file formats include *.baf, *.yep and *.fid file formats. SimGlycan® can now fragment peptides for a known glycopeptide sequence. By providing the peptide mass or the peptide sequence along with the site of glycosylation, amino acids modifications such as Cysteine modification, position of the modified amino acids, SimGlycan® generates all the probable fragments, enabling a user to check the presence amino acids by comparing it with the available experimental data.

SimGlycan® 2.55 Released

The new version brings you enhanced accuracy in search result by allowing you to specify the number of antennae, reducing terminal monosaccharide and non-reducing terminal monosaccharides expected for a structure. Seamless integration with ABI mass spectrometers will now enable you to open *.wiff and *.t2d files directly in SimGlycan®, without the use of third party converters. SimGlycan® is compatible with the AB Sciex mass spectrometers, including the 4800 Plus MALDI TOF/TOF™ Analyzer, the 4000 QTRAP® System and the QSTAR® Elite System. The SimGlycan® database is now updated with thousands of new glycan entries to provide more comprehensive search results.

SimGlycan® 2.51 Released

SimGlycan® now also analyzes glycopeptides in addition to released glycans. You can quickly resolve the structure of a glycan in a glycopeptide molecule by specifying the sequence or mass of the attached peptide moiety. The new version also supports 20 more monosaccharides, over the existing 42.

SimGlycan® 2.50 Released

You can now generate scatter and column plots, specify an m/z range to display specific plot sections and export plots for sharing results with your colleagues or for publication purposes. SimGlycan® now enables you to search for glycans with chemical derivatives used for reducing end modifications even if the derivative is not available in the program's database. For example, say you are working with 2AB (2-aminobenzamide) labeled glycans and SimGlycan® does not have it listed as a derivative, simply enter the mass. SimGlycan® would analyze all possible combinations in the database and display a list of the most closely matched glycans in a ranked order. You can now load MS/MS data in standard mzXML and mzData file formats. Using third party tools, the data from any mass spectrometer can be converted to mzData and mzXML, enabling SimGlycan® to seamlessly integrate with your mass spectrometer output. SimGlycan® now also supports MS/MS data generated on multi-charged ions.

SimGlycan® 2.21 Released

The upgrade includes improved data handling capabilities for SimGlycan®. Users can now expect better and faster search results using the product's new improved search algorithm.

SimGlycan® 2.20 Released

The upgrade includes the ability to search for glycans based on their ID, sequence, composition or mass. SimGlycan® displays the glycan structure, fragments, mass, class, reaction and pathway.
In addition, you can rename the Glycan ID and the MS profile to a name of your choice amongst a host of other improvements to give you better and faster results.

SimGlycan® 2.10 Released

With SimGlycan® 2.10, you will be able to select the proposed structures of interest manually. The program highlights the experimental m/z values that match those of theoretical fragments for easy selection and then generates an instant annotated stick spectrum or MS profile of them. It also enables you to assign your own rank to predicted structures, add comments and search fragments by their mass, name and m/z values.

SimGlycan® 2.00 Released

The upgrade includes support for sodium as an adduct and support for 16 more monosaccharides, over the existing 26.

SimGlycan® 1.50 Released

Export Results: With SimGlycan® 1.50, you can export glycan search results and generate an attractively formatted report for viewing or printing. Text File Input: Supports text file format for loading MS/MS data in addition to excel files. Manual MS/MS Data Input: You can manually type-in or copy/paste the MS/MS data into SimGlycan®. Database Updates: Supports additional monosaccharides.

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