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List of works by Bas van Breukelen

A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing.

scientific article

An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas.

scientific article

Analysis of the cGMP/cAMP interactome using a chemical proteomics approach in mammalian heart tissue validates sphingosine kinase type 1-interacting protein as a genuine and highly abundant AKAP.

scientific article published on June 2006

Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes

scientific article published on October 2008

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

scientific article

Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins.

scientific article published on 27 March 2014

Database independent proteomics analysis of the ostrich and human proteome.

scientific article published on 22 December 2011

Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides.

scientific article published on 15 May 2011

Deep Proteome Profiling of Circulating Granulocytes Reveals Bactericidal/Permeability-Increasing Protein as a Biomarker for Severe Atherosclerotic Coronary Stenosis

Evaluating experimental bias and completeness in comparative phosphoproteomics analysis.

scientific article

Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS.

scientific article published on 30 June 2014

Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster.

scientific article published on 23 November 2007

Identification of enriched PTM crosstalk motifs from large-scale experimental data sets.

scientific article

Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra.

scientific article

In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling

scientific article

LysNDeNovo: an algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation

scientific article published in March 2010

Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites

scientific article published on 17 April 2008

On-the-fly targeted selection of labeled peptides in liquid chromatography/mass spectrometry based quantitative proteomics

scientific article published on 01 January 2010

Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo

scientific article

Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels

scientific article

Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome

scientific article

Protease bias in absolute protein quantitation.

scientific article published on 30 May 2012

Proteogenomic Features of the Highly Polymorphic Histidine-rich Glycoprotein (HRG) Arose Late in Evolution

Proteome Adaptation of Saccharomyces cerevisiae to Severe Calorie Restriction in Retentostat Cultures

article

Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis.

scientific article published on 27 November 2013

Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes

scientific article published in November 2007

ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma

scientific article

Resolving stoichiometries and oligomeric states of glutamate synthase protein complexes with curve fitting and simulation of electrospray mass spectra

article

RockerBox: analysis and filtering of massive proteomics search results.

scientific article

Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution.

scientific article

StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry

scientific article

Targeted analysis of protein termini.

scientific article

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)

qcML: an exchange format for quality control metrics from mass spectrometry experiments

scientific article published on 23 April 2014

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