Literature DB >> 15215392

GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates.

Klaus Karl Lohmann1, Claus-W von der Lieth.   

Abstract

In recent years, mass spectrometry has become the method of choice for high-sensitivity glycan identification. Currently, only a few tools assisting mass spectra interpretation are available. The web application GlycoFragment (www.dkfz.de/spec/projekte/fragments/) calculates all theoretically possible fragments of complex carbohydrates and aims to support the interpretation of mass spectra. GlycoSearchMS (www.dkfz.de/spec/glycosciences.de/sweetdb/ms/) compares each peak of a measured mass spectrum with the calculated fragments of all structures contained in the SweetDB database. The best-matching spectra and the associated structures are displayed in order of decreasing similarity. Since both algorithms work very efficiently, they are well suited to be used for automatic identification of series of mass spectra of complex carbohydrates.

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Year:  2004        PMID： 15215392      PMCID： PMC441530          DOI： 10.1093/nar/gkh392

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  17 in total

Review 1.  Glycosylation and the immune system.

Authors:  P M Rudd; T Elliott; P Cresswell; I A Wilson; R A Dwek
Journal:  Science       Date:  2001-03-23       Impact factor: 47.728

Review 2.  Glycosylation analysis of gel-separated proteins.

Authors:  B Küster; T N Krogh; E Mørtz; D J Harvey
Journal:  Proteomics       Date:  2001-02       Impact factor: 3.984

Review 3.  Glycosylation and prion protein.

Authors:  Pauline M Rudd; Anthony H Merry; Mark R Wormald; Raymond A Dwek
Journal:  Curr Opin Struct Biol       Date:  2002-10       Impact factor: 6.809

4.  SWEET-DB: an attempt to create annotated data collections for carbohydrates.

Authors:  Alexander Loss; Peter Bunsmann; Andreas Bohne; Annika Loss; Eberhard Schwarzer; Elke Lang; Claus-W von der Lieth
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  GlycoMod--a software tool for determining glycosylation compositions from mass spectrometric data.

Authors:  C A Cooper; E Gasteiger; N H Packer
Journal:  Proteomics       Date:  2001-02       Impact factor: 3.984

Review 6.  Identification of protein-bound carbohydrates by mass spectrometry.

Authors:  D J Harvey
Journal:  Proteomics       Date:  2001-02       Impact factor: 3.984

7.  A high-performance liquid chromatography based strategy for rapid, sensitive sequencing of N-linked oligosaccharide modifications to proteins in sodium dodecyl sulphate polyacrylamide electrophoresis gel bands.

Authors:  P M Rudd; C Colominas; L Royle; N Murphy; E Hart; A H Merry; H F Hebestreit; R A Dwek
Journal:  Proteomics       Date:  2001-02       Impact factor: 3.984

8.  SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides.

Authors:  A Bohne; E Lang; C W von der Lieth
Journal:  Bioinformatics       Date:  1999-09       Impact factor: 6.937

9.  Sequencing of tri- and tetraantennary N-glycans containing sialic acid by negative mode ESI QTOF tandem MS.

Authors:  Dijana Sagi; Jasna Peter-Katalinic; Harald S Conradt; Manfred Nimtz
Journal:  J Am Soc Mass Spectrom       Date:  2002-09       Impact factor: 3.109

10.  Structural analysis of glycoconjugates by on-target enzymatic digestion and MALDI-TOF-MS.

Authors:  H Geyer; S Schmitt; M Wuhrer; R Geyer
Journal:  Anal Chem       Date:  1999-01-15       Impact factor: 6.986
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  31 in total

1.  Congruent strategies for carbohydrate sequencing. 2. FragLib: an MSn spectral library.

Authors:  Hailong Zhang; Suddham Singh; Vernon N Reinhold
Journal:  Anal Chem       Date:  2005-10-01       Impact factor: 6.986

2.  Automated interpretation of MS/MS spectra of oligosaccharides.

Authors:  Haixu Tang; Yehia Mechref; Milos V Novotny
Journal:  Bioinformatics       Date:  2005-06       Impact factor: 6.937

3.  Electron detachment dissociation of neutral and sialylated oligosaccharides.

Authors:  Julie T Adamson; Kristina Håkansson
Journal:  J Am Soc Mass Spectrom       Date:  2007-09-14       Impact factor: 3.109

4.  Automatic determination of O-glycan structure from fragmentation spectra.

Authors:  David Goldberg; Marshall Bern; Bensheng Li; Carlito B Lebrilla
Journal:  J Proteome Res       Date:  2006-06       Impact factor: 4.466

Review 5.  Automated glycopeptide analysis--review of current state and future directions.

Authors:  David C Dallas; William F Martin; Serenus Hua; J Bruce German
Journal:  Brief Bioinform       Date:  2012-07-27       Impact factor: 11.622

Review 6.  Protein analysis by shotgun/bottom-up proteomics.

Authors:  Yaoyang Zhang; Bryan R Fonslow; Bing Shan; Moon-Chang Baek; John R Yates
Journal:  Chem Rev       Date:  2013-02-26       Impact factor: 60.622

7.  Glycan family analysis for deducing N-glycan topology from single MS.

Authors:  David Goldberg; Marshall Bern; Simon J North; Stuart M Haslam; Anne Dell
Journal:  Bioinformatics       Date:  2008-12-10       Impact factor: 6.937

8.  The glycolyzer: automated glycan annotation software for high performance mass spectrometry and its application to ovarian cancer glycan biomarker discovery.

Authors:  Scott R Kronewitter; Maria Lorna A De Leoz; John S Strum; Hyun Joo An; Lauren M Dimapasoc; Andrés Guerrero; Suzanne Miyamoto; Carlito B Lebrilla; Gary S Leiserowitz
Journal:  Proteomics       Date:  2012-08       Impact factor: 3.984

Review 9.  Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2003-2004.

Authors:  David J Harvey
Journal:  Mass Spectrom Rev       Date:  2009 Mar-Apr       Impact factor: 10.946

Review 10.  Bioinformatics and molecular modeling in glycobiology.

Authors:  Martin Frank; Siegfried Schloissnig
Journal:  Cell Mol Life Sci       Date:  2010-04-04       Impact factor: 9.261
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