Literature DB >> 16478117

SearchXLinks. A program for the identification of disulfide bonds in proteins from mass spectra.

Stephan Wefing1, Volker Schnaible, Daniel Hoffmann.   

Abstract

We present the computer program SearchXLinks that analyzes mass spectra with the aim of identifying disulfide bonds and other modifications in proteins of known amino acid sequence. Disulfide bonds can be intra- or intermolecular. To decrease the number of false positives, the analysis of in-source decay and tandem mass spectra are coupled into the program. The steps taken during a SearchXLinks run are outlined, and the computational costs are discussed. The application of the program is illustrated by the analysis of data from recent studies on bovine ribonuclease A and bovine serum albumin. The software can be used free of charge on the Internet at http://www.searchxlinks.de.

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Year:  2006        PMID： 16478117     DOI： 10.1021/ac051634x

Source DB:  PubMed          Journal:  Anal Chem        ISSN： 0003-2700            Impact factor:   6.986


  12 in total

1.  Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D.

Authors:  Daniele Fabris; Eizadora T Yu
Journal:  J Mass Spectrom       Date:  2010-08       Impact factor: 1.982

2.  CrossSearch, a user-friendly search engine for detecting chemically cross-linked peptides in conjugated proteins.

Authors:  Owen W Nadeau; Gerald J Wyckoff; Justin E Paschall; Antonio Artigues; Jessica Sage; Maria T Villar; Gerald M Carlson
Journal:  Mol Cell Proteomics       Date:  2008-02-16       Impact factor: 5.911

3.  Collision induced dissociation products of disulfide-bonded peptides: ions result from the cleavage of more than one bond.

Authors:  Daniel F Clark; Eden P Go; Melinda L Toumi; Heather Desaire
Journal:  J Am Soc Mass Spectrom       Date:  2011-02-05       Impact factor: 3.109

Review 4.  Protein Structural Analysis via Mass Spectrometry-Based Proteomics.

Authors:  Antonio Artigues; Owen W Nadeau; Mary Ashley Rimmer; Maria T Villar; Xiuxia Du; Aron W Fenton; Gerald M Carlson
Journal:  Adv Exp Med Biol       Date:  2016       Impact factor: 2.622

5.  Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry.

Authors:  Xiuxia Du; Saiful M Chowdhury; Nathan P Manes; Si Wu; M Uljana Mayer; Joshua N Adkins; Gordon A Anderson; Richard D Smith
Journal:  J Proteome Res       Date:  2011-02-16       Impact factor: 4.466

6.  Analysis of the disulfide bond arrangement of the HIV-1 envelope protein CON-S gp140 ΔCFI shows variability in the V1 and V2 regions.

Authors:  Eden P Go; Ying Zhang; Sushma Menon; Heather Desaire
Journal:  J Proteome Res       Date:  2010-12-30       Impact factor: 4.466

7.  Gas-phase scrambling of disulfide bonds during matrix-assisted laser desorption/ionization mass spectrometry analysis.

Authors:  Liang Zhao; Ruben T Almaraz; Fan Xiang; Jerry L Hedrick; Andreas H Franz
Journal:  J Am Soc Mass Spectrom       Date:  2009-05-13       Impact factor: 3.109

8.  Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engine.

Authors:  Hua Xu; Liwen Zhang; Michael A Freitas
Journal:  J Proteome Res       Date:  2007-12-12       Impact factor: 4.466

9.  Molecular basis of catalytic chamber-assisted unfolding and cleavage of human insulin by human insulin-degrading enzyme.

Authors:  Marika Manolopoulou; Qing Guo; Enrico Malito; Alexander B Schilling; Wei-Jen Tang
Journal:  J Biol Chem       Date:  2009-03-25       Impact factor: 5.157

10.  Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome.

Authors:  Richard J Grainger; J David Barrass; Alain Jacquier; Jean-Christophe Rain; Jean D Beggs
Journal:  RNA       Date:  2009-10-23       Impact factor: 4.942
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