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A computational tool set developed to tackle the heart of the problems in MS(2) sequencing of glycopeptide. It accepts low resolution and low accuracy ion trap MS(2) data, filters for glycopeptides, couples knowledge-based de novo interpretation of glycosylation-dependent fragmentation pattern with protein database search, and uses machine-learning algorithm to score the computed glyco and peptide combinations. Higher ranking candidates are then compiled into a list of MS(2)/MS(3) entries to drive subsequent rounds of targeted MS(3) sequencing of putative peptide backbone, allowing its validation by database search in a fully automated fashion. With additional fishing out of all related glycoforms and final data integration, the platform proves to be sufficiently sensitive and selective, conducive to novel glycosylation discovery, and robust enough to discriminate, among others, N-glycolyl neuraminic acid/fucose from N-acetyl neuraminic acid/hexose.
MAGIC / Mass spectrometry-based Automated Glycopeptide IdentifiCation platform
Identifies intact N-glycosylated peptides from a public protein database without requiring any prior information of proteins or glycans. MAGIC aims to support untargeted glycopeptide analysis while the newly implemented MAGIC+ is designed to perform targeted glycopeptide analysis that allows users to upload their own protein sequence file to find glycopeptides in their data. The search results from Mascot can be integrated with the results from MAGIC-web via Reports Integrator to generate a complete protein/peptide-glycan summary report. Independent of the above three modules, the fourth module, Glycan Search, allows users to find various glycans from a large glycan database stored in the web server, regardless the types of glycosylation. MAGIC-web has a user-friendly visualization interface for easy data uploading and processing, and result interpretation. MAGIC-web is free and open to all users and there is no log in requirement.
Allows the drawing of glycan structures. GlycanBuilder is a glycan visualization tool developed during the EUROCarbDB project. The software supports drawing of ambiguous glycan structures including unknown configurations and linkages, glycan fragments, probability annotations, monosaccharide compositions and superclasses of monosaccharides. The glycans can also be displayed as images using Symbol Nomenclature for Glycans (SNFG) symbols. GlycanBuilder is also part of GlyS3, as a web application.
Enables easy generation of all theoretically possible fragments of a defined glycan structure. GlycoFragment supports the assignment of all peaks contained in a mass spectrum. It calculates the mass of all possible fragments of an oligosaccharide in three steps: (i) a complete topological description of all atoms and their connectivity is generated, (ii) the molecular structure is analysed and bonds, and (iii) each possible fragment is generated by virtual bond cleavage and a subsequent summation of atomic masses of the atoms belonging to a certain fragment.
GIGtool / glycoprotein immobilization for glycan extraction
Browses N-linked and O-linked glycans in LC-MS/MS experiment. GIG Tool is an application that extracts (i) precursor masses, (ii) oxonium ions and glycan fragments from tandem (liquid chromatography (LC)–MS/MS) mass spectra for glycan identification, and (iii) reporter ions from quaternary amine containing isobaric tag for glycan (QUANTITY) isobaric tags. These data are used for quantification of the relative abundance of N-glycans.
GLYCH / GLYcan CHaracterization
A package for glycan characterization using MS/MS. GLYCH consists of three steps. First, we develop a scoring scheme to identify potential bond linkages between monosaccharides, based on the appearance pattern of cross-ring ions. Next, we use a dynamic programming algorithm to determine the most probable oligosaccharide structures from the mass spectrum. Finally, we re-evaluate these oligosaccharide structures, taking into account the double fragmentation ions.
GlycoPep DB
A web-based tool, GlycoPep DB, designed to facilitate compositional assignment for glycopeptides by comparing experimentally measured masses to all calculated glycopeptide masses from a carbohydrate database with N-linked glycans. GlycoPep DB is an advance over current tools to assign N-linked glycans because it uses a concept of "smart searching", where only biologically relevant carbohydrate compositions are searched, when matching carbohydrate compositions with the MS data making glycopeptide compositional assignment more efficient.
A framework to characterize glycopeptides in biological proteome samples using the scoring of complementary fragmentation techniques, including collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD). In addition to filtering glycopeptide ions based on HCD scoring, the framework utilizes scoring schemes of ETD spectrum (to determine the peptide sequence) and a glycan sequencing algorithm from CID spectrum (to characterize the glycan). The term “glycan sequence” is used here to indicate a cartoon-graph representation of glycans that contain monosaccharide composition and topology. The algorithm of constructing the topological arrangement of monosaccharides from CID spectra is referred to as “glycan sequencing”.
GP Finder / GlycoPeptide Finder
Implements an algorithm to assign glycopeptide identities (peptide structure + glycan composition) by their fragmentation mass spectra. While candidate glycopeptides can be found with a single tandem mass spectrum, statistical significance of assignments as stated by a false discovery rate can be determined using decoy analysis. As implemented in GP Finder 3, decoy analysis requires input from many spectra taken in a single session, thus, in order to use decoy analysis, GP Finder 3 requires data be provided as with mass-chromatograms.
Implements a heuristic iterated glycan sequencing algorithm coupled with prior knowledge for automated elucidation of the glycan structure within a glycopeptide from its collision-induced dissociation tandem mass spectrum. GlycoSeq employs rules of glycosidic linkage as defined by glycan synthetic pathways to eliminate improbable glycan structures and build reasonable glycan trees. We tested the tool on two sets of tandem mass spectra of N-linked glycopeptides cell lines acquired from breast cancer patients. After employing enzymatic specificity within the N-linked glycan synthetic pathway, the sequencing results of GlycoSeq were highly consistent with the manually curated glycan structures. Hence, GlycoSeq is ready to be used for the characterization of glycan structures in glycopeptides from MS/MS analysis.
GlyQ-IQ / Glycomics Quintavariate-Informed Quantification
A software application for glycan MS based upon an algorithm centric nontargeted analyses approach. Combining spectral averaging, mass-independent fit score calculations, tight fit score tolerances, and a 1 Da interfering peak deconvolution result in over 99% of all glycans identified passed manual inspection and juxtaposition to high-resolution mass spectra. In addition to high specificity LC–MS feature detection, key integration of glycan relationships and insource fragmentation detection further increased the annotation confidence and decreased the false positive rate.
A web-based bioinformatic tool designed to link glycomics and proteomics analyses for the characterization of glycopeptides. GlycoSpectrumScan is MS-platform independent, freely accessible, and profiles glycopeptide MS data using beforehand separately acquired released glycan and proteomics information. Both N- and O-glycosylated peptides as well as multiply glycosylated peptides can be analyzed. It has been successfully applied and tested on the human colostrum sIgA glycoprotein complex.
Aids in the interpretation of MS data from a nonspecific protease treatment of a glycoprotein. The determination includes both the occupation of the site and site heterogeneity. The GlycoX program has three main functions, a ‘glycosylation site search’ for the determination of glycosylation sites with oligosaccharide heterogeneity in glycoproteins; an ‘oligosaccharide calculator’ for assigning oligosaccharide compositions for N-linked, O-linked, and chemically modified oligosaccharides; and an ‘auto-isotope filter’ for selecting the monoisotopic peaks from the mass spectra of glycopeptides, peptides, and glycans.
A graph-based spectral alignment algorithm that can identify glycopeptides with multiple hydroxylysine O-glycosylation sites by tandem mass spectra. GlycoMID was designed for the identification of glycopeptides, not for the computation of localization scores of glycosylation sites. For an MS/MS spectrum, it reports only a best scoring glycopeptide with its glycosylation sites and structures, not localization scores of the identified glycosylation sites. GlycoMID was tested on mass spectrometry data sets of the bovine collagen alpha-(II) chain protein, and experimental results showed that it identified more glycopeptide-spectrum matches than other existing tools, including many glycopeptides with two glycosylation sites.
Permits to obtain peptide backbone identification and glycan False Discovery Rate (FDR) estimation. pGlyco is a pipeline that includes two features: (i) complementary fragments from both Higher-energy Collisional Dissociation-tandem mass spectrometry (HCD-MS/MS) and Collision-Induced Dissociation-tandem mass spectrometry (CID-MS/MS) used to identify glycans, and (ii) data-dependent acquisition (DDA) of MS3 for some most intense peaks in the HCD-MS/MS spectrum used to identify peptide backbones. By combining these features, intact glycopeptides could be identified with detailed spectral information for both glycans and peptides.
GDG / Glycopeptide Decoy Generator
Enables determination of the accuracy of tools that assign glycopeptides to collision-induced dissociation (CID) data. GDG is a graphical method to generate glycopeptide decoys de novo. The software can also be easily incorporated into other bioinformatics tools designed to match glycopeptides to CID data. The decoys generated by GDG can be divided into three categories based on their glycan compositions: (i) decoys containing [HexNAc]2[Hex]1-n[Fuc]0-2, (ii) decoys containing [NeuNAc] and (iii) decoy glycopeptides not belonging to first categories.
ProSight Lite
A free Windows application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Fixed or variable modifications, including both PTMs and a select number of glycosylations, can be applied to the amino acid sequence. The application reports multiple scores and a matching fragment list. Fragmentation maps can be exported for publication in either portable network graphic (PNG) or scalable vector graphic (SVG) format.
An open-source Java library for the analysis of mass spectrometry data from large scale proteomics and glycomics experiments. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce and Apache Spark frameworks for cluster computing was implemented.
Predicts and scores candidate compounds based on quantitative features derived from calculations. GlycReSoft is an algorithm that provides both rapid extraction of glycan compositions from the Decon2LS output as well as a means of scoring the results to facilitate confident use of glycomics Liquid Chromatography/Mass Spectrometry (LC/MS) data. This application implements supervised and unsupervised scoring methods that enable assignment of peaks to both known and unknown glycan compositions.
Galaxy / Glycoanalysis by the three axes of MS and Chromatography
Provides a useful method for an analytical procedure for N-glycan structures. Galaxy is a 2D/3D mapping method developed for the structural determination of asparagine-linked oligosaccharides (N-glycans) in glycoproteins. The structure of a sample PA-glycan can be estimated by comparing its elution position on the map with the positions of the known reference N-glycans plotted on the 2D map. This application can also be used as a means of isolating large-scale samples for nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry (MS) spectrometry.
Increases the capacity to recognize and deconvolute overlapped glycan isotopic clusters. GlycoMaid is a matching glycan isotope abundance that exhibits significant improvement in sensitivity, accuracy and user-friendliness for automatic identification and annotation of glycan profiles. Furthermore, mGIA algorithm is improved by introducing an optimization model and an automatic composition matching process that can recognize and deconvolute the overlapping glycan isotopic clusters. The separated isotope clusters are then processed with mGIA algorithm and identified by GlycoMaid.
Permits users to conduct high throughput, semi-quantitative glycotope-centric glycomic mapping for MS2/MS3 spectra. GlyPick aims to delineate the various isomeric glycotopes by well-established diagnostic ions. It is able to mass fit the m/z values of identified monoisotopic precursors to glycosyl compositions. This tool gathers functions to customize adducts, modifications, maximum and minimum number of allowed glycosyl residues, and simple rules of permissible combination derived from biosynthetic constrains.
GPG / GlycoPep grader
A software analysis tool to increase the speed and efficiency of assigning N-linked glycopeptide composition from MS/MS data. GPG relies on the identification of unique dissociation patterns shown for high mannose, hybrid, and complex N-linked glycoprotein types, including patterns specific to those structures containing fucose or sialic acid residues. The novel GPG scoring algorithm scores potential candidate compositions of the same nominal mass against MS/MS data through evaluation of the Y(1) ion and other peptide-containing product ions, across multiple charge states, when applicable. In addition to evaluating the peptide portion of a given glycopeptide, the GPG algorithm predicts and scores product ions that result from unique neutral losses of terminal glycans.
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