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Glycosylation identification software tools| MS-based untargeted proteomics

Glycosylation is one of the most commonly observed post-translational modifications (PTMs) in eukaryotes. It is believed that more than 50% eukaryotic proteins are glycosylated. To reveal the biological functions of protein-linked glycans involved…
GlycoFragment
Web

GlycoFragment

Enables easy generation of all theoretically possible fragments of a defined…

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…

Sweet-Heart
Desktop

Sweet-Heart

A computational tool set developed to tackle the heart of the problems in MS(2)…

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,…

GIGtool
Desktop

GIGtool glycoprotein immobilization for glycan extraction

Browses N-linked and O-lined glycans in LC-MS/MS experiment. GIG Tool is an…

Browses N-linked and O-lined 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…

GlycoMod
Web

GlycoMod

Finds all possible compositions of a glycan structure from its experimentally…

Finds all possible compositions of a glycan structure from its experimentally determined mass. GlycoMod is a web application which can be used to predict the composition of any glycoprotein derived…

GlySeq
Web

GlySeq

Analyses the statistics of amino acids in the sequential neighborhood of N- and…

Analyses the statistics of amino acids in the sequential neighborhood of N- and O-glycosylation sites. GlySeq is a software for a statistical analysis of the amino acid composition around…

GPQuest
Desktop

GPQuest

Provides automatic identification of intact glycopeptides from Higher-energy…

Provides automatic identification of intact glycopeptides from Higher-energy Collisional Dissociation (HCD) spectra of complex biological samples based on spectral library matching. GPQuest is an…

GlycoSearchMS
Web

GlycoSearchMS

Compares a measured mass spectrum with a library of calculated spectra. The…

Compares a measured mass spectrum with a library of calculated spectra. The GlycoFragment compares each peak of the input spectrum with the calculated fragments of all structures contained in its…

MAGIC
Web
Desktop

MAGIC Mass spectrometry-based Automated Glycopeptide IdentifiCation platform

Identifies intact N-glycosylated peptides from a public protein database…

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…

SugarQb
Desktop

SugarQb

Enables genome-wide insights into protein glycosylation and glycan…

Enables genome-wide insights into protein glycosylation and glycan modifications in complex biological systems. SugarQb identifies intact glycopeptides, and maps and quantifies changes in protein…

pGlyco
Desktop

pGlyco

Permits to obtain peptide backbone identification and glycan False Discovery…

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…

GDG
Desktop

GDG Glycopeptide Decoy Generator

Enables determination of the accuracy of tools that assign glycopeptides to…

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…

GlycoSeq
Desktop

GlycoSeq

Implements a heuristic iterated glycan sequencing algorithm coupled with prior…

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…

gFinder
Web

gFinder

Analyzes mixtures of native N glycopeptides that have been profiled by tandem…

Analyzes mixtures of native N glycopeptides that have been profiled by tandem mass spectrometry. gFinder provides features to identify successfully glycopeptides present in not only standard…

GRITS Toolbox
Desktop

GRITS Toolbox

Enables high throughput comprehensive characterization of glycosylation where…

Enables high throughput comprehensive characterization of glycosylation where analysis of site of glycan attachment is important. GRITS Toolbox combines the analytical power of glycan permethylation…

DrawGlycan-SNFG
Web
Desktop

DrawGlycan-SNFG

Assists users in simply drawing glycans. DrawGlycan-SNFG is a simple program…

Assists users in simply drawing glycans. DrawGlycan-SNFG is a simple program where users can rapidly display glycan and peptide bond fragmentations using simply International Union of Pure and…

GlycoProteomics…
Desktop

GlycoProteomics Analysis Toolbox

Provides a method for glycoproteomics data analysis. GlycoPAT is a software…

Provides a method for glycoproteomics data analysis. GlycoPAT is a software that presents concepts and functions for glycopeptide digestion, database generation, glycopeptide fragmentation, spectrum…

GlycoDeNovo
Desktop

GlycoDeNovo

Provides a computational method to establish glycan topologies from associated…

Provides a computational method to establish glycan topologies from associated mass spectra. GlycoDeNovo provides an interpretation-graph which designates how to interpret each peak until the…

GlyS3
Web

GlyS3

Matches any substructure such as glycan determinants to a large collection of…

Matches any substructure such as glycan determinants to a large collection of structures recorded in UniCarbKB, SugarBindDB or GlycomeDB. Glys3 allows to draw glycan structures. A text interface is…

NGlycPred Server
Web

NGlycPred Server N-linked Glycosylation Prediction Server

Identifies the N-X-T/S sequons from the given input protein data bank (PDB)…

Identifies the N-X-T/S sequons from the given input protein data bank (PDB) file and predicts the glycan occupancy of each sequon. NGlycPred utilizes both structural as well as residue pattern…

GlycoProfileAss…
Desktop

GlycoProfileAssigner

A software tool to automatically assign structures to HPLC/UPLC glycan…

A software tool to automatically assign structures to HPLC/UPLC glycan analytical data. GlycoProfileAssigner does this by initially assigning possible glycan structures to LC peaks by GU values.…

GlycanAnalysis
Desktop

GlycanAnalysis

Searches a glycan database to support the identification of glycan structures…

Searches a glycan database to support the identification of glycan structures from MS/MS spectra. It also calculates diagnostic ions of glycan structures registered in a glycan database (GlycomeDB or…

GlycoMID
Desktop

GlycoMID

A graph-based spectral alignment algorithm that can identify glycopeptides with…

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…

GlycoMaid
Desktop

GlycoMaid

Increases the capacity to recognize and deconvolute overlapped glycan isotopic…

Increases the capacity to recognize and deconvolute overlapped glycan isotopic clusters. GlycoMaid is a matching glycan isotope abundance that exhibits significant improvement in sensitivity,…

GlycoFragwork
Desktop

GlycoFragwork

A framework to characterize glycopeptides in biological proteome samples using…

A framework to characterize glycopeptides in biological proteome samples using the scoring of complementary fragmentation techniques, including collision-induced dissociation (CID), higher-energy…

GlyQ-IQ
Desktop

GlyQ-IQ Glycomics Quintavariate-Informed Quantification

A software application for glycan MS based upon an algorithm centric…

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,…

GPE
Desktop

GPE GlycoPep Evaluator

A tool that helps to measure FDRs in identifying glycopeptides without using a…

A tool that helps to measure FDRs in identifying glycopeptides without using a decoy database.

GlycoDigest
Desktop
Web

GlycoDigest

A tool that simulates exoglycosidase digestion, based on controlled rules…

A tool that simulates exoglycosidase digestion, based on controlled rules acquired from expert knowledge and experimental evidence available in GlycoBase. The tool allows the targeted design of…

GlycanBuilder
Desktop

GlycanBuilder

An intuitive and flexible software tool for building and displaying glycan…

An intuitive and flexible software tool for building and displaying glycan structures.

GlycanMass
Web

GlycanMass

Allows to calculate the mass of an oligosaccharide structure from its…

Allows to calculate the mass of an oligosaccharide structure from its oligosaccharide composition. GlycanMass uses hexose, HexNAc, deoxyhexose, NeuAc, NeuGc, pentose, sulfate, phosphate, KDN and HexA…

SweetSEQer
Desktop

SweetSEQer

A method for simple de novo identification and sequencing of glycoconjugate…

A method for simple de novo identification and sequencing of glycoconjugate spectra. It generates spectral annotations and graphical annotation figures.

GP Finder
Desktop

GP Finder GlycoPeptide Finder

Implements an algorithm to assign glycopeptide identities (peptide structure +…

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…

GlycoPep ID
Web

GlycoPep ID

Correlates product ions in collision-induced dissociation (CID) experiments of…

Correlates product ions in collision-induced dissociation (CID) experiments of suspected glycopeptides to a peptide composition. After identifying the peptide portion of glycopeptides with GlycoPep…

GPG
Web

GPG GlycoPep grader

A software analysis tool to increase the speed and efficiency of assigning…

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…

GlycoPep DB
Web

GlycoPep DB

A web-based tool, GlycoPep DB, designed to facilitate compositional assignment…

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…

GPD
Web

GPD GlycoPep Detector

It filters out noise peaks that interfere with glycopeptide sequencing,…

It filters out noise peaks that interfere with glycopeptide sequencing, correlates input glycopeptide compositions with the ETD spectra, and assigns a score for each candidate.

GLYCH
Desktop

GLYCH GLYcan CHaracterization

A package for glycan characterization using MS/MS. GLYCH consists of three…

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…

MultiGlycan
Desktop

MultiGlycan

Helps user to gather glycan profile information from LC-MS Spectra. It also…

Helps user to gather glycan profile information from LC-MS Spectra. It also reports quantity of specific glycan composition.

GlycoX
Desktop

GlycoX

Aids in the interpretation of MS data from a nonspecific protease treatment of…

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…

GlycoSpectrumSc…
Web

GlycoSpectrumScan

A web-based bioinformatic tool designed to link glycomics and proteomics…

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…

Peptoonist
Desktop

Peptoonist

A program that can automatically identify the glycans (sugars) present at each…

A program that can automatically identify the glycans (sugars) present at each N-glycosylation site of a protein. The input to Peptoonist is a series of mass spectra, both MS and MS/MS, obtained from…

GPS
Desktop

GPS GlycoPeptideSearch

Simplifies data interpretation of N-glycopeptide CID MS/MS datasets by…

Simplifies data interpretation of N-glycopeptide CID MS/MS datasets by searching for glycopeptide results consistent with MS/MS spectra.

GlycReSoft
Desktop

GlycReSoft

Predicts and scores candidate compounds based on quantitative features derived…

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…

XGlycScan
Desktop

XGlycScan

Mass spectrometry based glycoproteomics has become a major means of identifying…

Mass spectrometry based glycoproteomics has become a major means of identifying and characterizing previously N-linked glycan attached loci (glycosites). XGlycScan maps varying length peptide species…

UniCarb-DB
Dataset

UniCarb-DB

A comprehensive LC MS/MS library of N- and O- linked glycans released from…

A comprehensive LC MS/MS library of N- and O- linked glycans released from glycoproteins that have been annotated with glycosidic and cross-ring fragmentation ions, retention times, and associated…

GlycoWorkbench
Desktop

GlycoWorkbench

A suite of software tools designed for the rapid drawing of glycan structures…

A suite of software tools designed for the rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data.

ISOGlyP
Web

ISOGlyP Isoform Specific O-Glycosylation Prediction

Provides isoform specific O-glycosylation prediction. ISOGlyP utilizes…

Provides isoform specific O-glycosylation prediction. ISOGlyP utilizes transferase specific enhancement values to perform predictive calculations giving the so-called enhancement value product (EVP).…

GlycoMiner
Desktop

GlycoMiner

A software tool to automatically identify tandem (MS/MS) spectra obtained in…

A software tool to automatically identify tandem (MS/MS) spectra obtained in liquid chromatography/mass spectrometry (LC/MS) runs which correspond to N-glycopeptides. The program complements…

SimGlycan
Desktop

SimGlycan

Predicts structure of glycans from the MS/MS and multi-stage mass spectrometry…

Predicts structure of glycans from the MS/MS and multi-stage mass spectrometry (MSn) data. Furthermore, comprehensive support for resolving glycopeptides using LC-MS/MS glycopeptide data facilitates…

autoGU
Desktop

autoGU

Provides an analytical tool to assist data interpretation to bring glycan…

Provides an analytical tool to assist data interpretation to bring glycan analysis within the reach of any well-established laboratory. autoGU is a database-matching software developed to…

EnsembleGly
Desktop

EnsembleGly

Identifies sites from amino acid sequence of proteins. EnsembleGly is a web…

Identifies sites from amino acid sequence of proteins. EnsembleGly is a web application for glycosylation site prediction that provides a server for prediction of O-, N-, and C-Linked glycosylation…

CKSAAP_OGlysite
Web

CKSAAP_OGlysite Composition of K-Spaced Amino Acid Pairs in O-glycosylation sites

Predicts mucin-type O-linked glycosylation sites in mammalian proteins.…

Predicts mucin-type O-linked glycosylation sites in mammalian proteins. CKSAAP_OGlySite is a web-server developed to facilitate the biological community. This resource demonstrates higher prediction…

GlycoMaster DB
Web

GlycoMaster DB

A software tool to assist the automated and high-throughput identification of…

A software tool to assist the automated and high-throughput identification of intact N-linked glycopeptides from MS/MS spectra.

XDB
Dataset

XDB Xeno-glycomics database

It includes comprehensive pig glycan information on structures, mass values…

It includes comprehensive pig glycan information on structures, mass values (m/z), types, relative quantities and biological sources.

GlyPID
Desktop

GlyPID

A targeted MS/MS analysis approach to guide multiple experiments, thus…

A targeted MS/MS analysis approach to guide multiple experiments, thus permitting a complete characterization of all N-glycosylation sites of glycoproteins present in a complex sample. This approach…

MonosaccharideD…
Dataset

MonosaccharideDB

It is intended to be a comprehensive resource of monosaccharides.

It is intended to be a comprehensive resource of monosaccharides.

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