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List of works by Lennart Martens

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ProteomeXchange provides globally coordinated proteomics data submission and dissemination

scientific article (publication date: March 2014)
The minimum information about a proteomics experiment (MIAPE)

scientific article (publication date: August 2007)
Improved visualization of protein consensus sequences by iceLogo

scholarly article by Niklaas Colaert et al published November 2009 in Nature Methods
LNCipedia: a database for annotated human lncRNA transcript sequences and structures

scientific article (publication date: 2013)
The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways

scientific article
mzML--a community standard for mass spectrometry data

2011 scientific article
PRIDE: the proteomics identifications database

scientific article
Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides

scientific article
The Proteomics Identifications database: 2010 update

scientific article (publication date: 2010)
A guide to the Proteomics Identifications Database proteomics data repository

scientific article (publication date: September 2009)
SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

scientific article published on 31 January 2011
LNCipedia 5: towards a reference set of human long non-coding RNAs

PRIDE: a public repository of protein and peptide identifications for the proteomics community

scientific article published in January 2006
Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis

scientific article published in October 2005
PRIDE Converter: making proteomics data-sharing easy

scientific article published on July 2009
Human Proteinpedia enables sharing of human protein data

scientific article
The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation.

scientific article
PRIDE Inspector: a tool to visualize and validate MS proteomics data

scientific article (publication date: 8 February 2012)
Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins

scientific article published on November 2002
PRIDE: new developments and new datasets

scientific article (publication date: 2008)
Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis

scientific article published on 20 April 2007
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

scientific article (publication date: 18 October 2007)
DBToolkit: processing protein databases for peptide-centric proteomics

scientific article published in 2005
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium

scientific article (publication date: December 2012)
The Ontology Lookup Service: bigger and better

scientific article (publication date: July 2010)
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

scientific article
The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile

scientific article published in August 2005
An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes

scientific article published on 18 December 2014
compomics-utilities: an open-source Java library for computational proteomics

scientific article
TraML--a standard format for exchange of selected reaction monitoring transition lists

scientific article published on 12 December 2011
ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics.

scientific article
Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18.

scientific article published in July 2004
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries

scientific article
Peptide and protein quantification: a map of the minefield.

scientific article published on February 2010
Unipept 4.0: Functional Analysis of Metaproteome Data

scientific article published on 04 December 2018
Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways.

scientific article
SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

scientific article published on 9 February 2018
A la carte proteomics with an emphasis on gel-free techniques

scientific article published on August 2007
jmzML, an open-source Java API for mzML, the PSI standard for MS data

scientific article
Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research

scientific article (publication date: 10 October 2010)
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project

scientific article
Getting intimate with trypsin, the leading protease in proteomics

scientific article published on 15 June 2013
Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering

scientific article
Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation

scientific article
The PSI semantic validator: a framework to check MIAPE compliance of proteomics data

scientific article
Current methods for global proteome identification

scientific article published on October 2012
A Golden Age for Working with Public Proteomics Data

scientific article
Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

scientific article
DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

scientific article published on 7 January 2014
Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies

scientific article published in April 2004

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