Literature DB >> 16030071

DBToolkit: processing protein databases for peptide-centric proteomics.

Lennart Martens1, Joël Vandekerckhove, Kris Gevaert.   

Abstract

UNLABELLED: DBToolkit is a user-friendly, easily extensible tool that allows the processing of protein sequence databases to peptide-centric sequence databases. This processing is primarily aimed at enhancing the useful information content of these databases for use as optimized search spaces for efficient identification of peptide fragmentation spectra obtained by mass spectrometry. In addition, DBToolkit can be used to reliably solve a range of other typical tasks in processing sequence databases. AVAILABILITY: DBToolkit is open source under the GNU GPL license. The source code, full user and developer documentation and cross-platform binaries are freely downloadable from the project website at http://genesis.UGent.be/dbtoolkit/ CONTACT: lennart.martens@UGent.be

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Year:  2005        PMID： 16030071     DOI： 10.1093/bioinformatics/bti588

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  43 in total

1.  Probing the efficiency of proteolytic events by positional proteomics.

Authors:  Kim Plasman; Petra Van Damme; Dion Kaiserman; Francis Impens; Kimberly Demeyer; Kenny Helsens; Marc Goethals; Phillip I Bird; Joël Vandekerckhove; Kris Gevaert
Journal:  Mol Cell Proteomics       Date:  2010-11-03       Impact factor: 5.911

2.  The wildcat toolbox: a set of perl script utilities for use in peptide mass spectral database searching and proteomics experiments.

Authors:  Paul A Haynes; Susan Miller; Tim Radabaugh; Michael Galligan; Linda Breci; James Rohrbough; Fatimah Hickman; Nirav Merchant
Journal:  J Biomol Tech       Date:  2006-04

3.  Challenges and solutions in proteomics.

Authors:  Huang Hongzhan; Hem D Shukla; Wu Cathy; Saxena Satya
Journal:  Curr Genomics       Date:  2007-03       Impact factor: 2.236

4.  Targeted peptidecentric proteomics reveals caspase-7 as a substrate of the caspase-1 inflammasomes.

Authors:  Mohamed Lamkanfi; Thirumala-Devi Kanneganti; Petra Van Damme; Tom Vanden Berghe; Isabel Vanoverberghe; Joël Vandekerckhove; Peter Vandenabeele; Kris Gevaert; Gabriel Núñez
Journal:  Mol Cell Proteomics       Date:  2008-07-30       Impact factor: 5.911

5.  Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis.

Authors:  Ileana R León; Veit Schwämmle; Ole N Jensen; Richard R Sprenger
Journal:  Mol Cell Proteomics       Date:  2013-06-21       Impact factor: 5.911

6.  N-terminomics identifies Prli42 as a membrane miniprotein conserved in Firmicutes and critical for stressosome activation in Listeria monocytogenes.

Authors:  Francis Impens; Nathalie Rolhion; Lilliana Radoshevich; Christophe Bécavin; Mélodie Duval; Jeffrey Mellin; Francisco García Del Portillo; M Graciela Pucciarelli; Allison H Williams; Pascale Cossart
Journal:  Nat Microbiol       Date:  2017-02-13       Impact factor: 17.745

7.  A Saccharomyces cerevisiae model reveals in vivo functional impairment of the Ogden syndrome N-terminal acetyltransferase NAA10 Ser37Pro mutant.

Authors:  Petra Van Damme; Svein I Støve; Nina Glomnes; Kris Gevaert; Thomas Arnesen
Journal:  Mol Cell Proteomics       Date:  2014-01-09       Impact factor: 5.911

8.  Identification of Protease Specificity by Combining Proteome-Derived Peptide Libraries and Quantitative Proteomics.

Authors:  Martin L Biniossek; Melanie Niemer; Ken Maksimchuk; Bettina Mayer; Julian Fuchs; Pitter F Huesgen; Dewey G McCafferty; Boris Turk; Guenther Fritz; Jens Mayer; Georg Haecker; Lukas Mach; Oliver Schilling
Journal:  Mol Cell Proteomics       Date:  2016-04-27       Impact factor: 5.911

9.  A Role for Human N-alpha Acetyltransferase 30 (Naa30) in Maintaining Mitochondrial Integrity.

Authors:  Petra Van Damme; Thomas V Kalvik; Kristian K Starheim; Veronique Jonckheere; Line M Myklebust; Gerben Menschaert; Jan Erik Varhaug; Kris Gevaert; Thomas Arnesen
Journal:  Mol Cell Proteomics       Date:  2016-09-30       Impact factor: 5.911

10.  Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster.

Authors:  Sandra Goetze; Ermir Qeli; Christian Mosimann; An Staes; Bertran Gerrits; Bernd Roschitzki; Sonali Mohanty; Eva M Niederer; Endre Laczko; Evy Timmerman; Vinzenz Lange; Ernst Hafen; Ruedi Aebersold; Joël Vandekerckhove; Konrad Basler; Christian H Ahrens; Kris Gevaert; Erich Brunner
Journal:  PLoS Biol       Date:  2009-11-03       Impact factor: 8.029
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