Publications by authors named "Bas van Breukelen"

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Proteogenomic Features of the Highly Polymorphic Histidine-rich Glycoprotein Arose Late in Evolution.
Yang Zou, Bas van Breukelen, Matti Pronker, Karli Reiding, Albert J R Heck

Mol Cell Proteomics· July 2023

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Identification of Protein Complexes by Integrating Protein Abundance and Interaction Features Using a Deep Learning Strategy.
Bohui Li, Maarten Altelaar, Bas van Breukelen

Int J Mol Sci· April 2023

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Schistosoma mansoni infection affects the proteome and lipidome of circulating extracellular vesicles in the host.
Michiel L Bexkens, Renske A van Gestel, Bas van Breukelen, Rolf T Urbanus, Jos F Brouwers

Mol Biochem Parasitol· July 2020

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Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution.
Mao Peng, Thin Thin Aye, Berend Snel, Bas van Breukelen, Arjen Scholten

J Proteome Res· July 2015

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An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas.
Piero Giansanti, Thin Thin Aye, Henk van den Toorn, Mao Peng, Bas van Breukelen

Cell Rep· June 2015

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ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma.
Marjon A Smit, Gianluca Maddalo, Kylie Greig, Linsey M Raaijmakers, Patricia A Possik, Bas van Breukelen

Mol Syst Biol· December 2014

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Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS.
Fan Liu, Bas van Breukelen, Albert J R Heck

Mol Cell Proteomics· October 2014

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Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins.
Ana C L Guerreiro, Marco Benevento, Robert Lehmann, Bas van Breukelen, Harm Post

Mol Cell Proteomics· August 2014

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qcML: an exchange format for quality control metrics from mass spectrometry experiments.
Mathias Walzer, Lucia Espona Pernas, Sara Nasso, Wout Bittremieux, Sven Nahnsen, Bas van Breukelen

Mol Cell Proteomics· August 2014

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Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures.
Nadine A Binai, Markus M M Bisschops, Bas van Breukelen, Shabaz Mohammed, Luuk Loeff

J Proteome Res· August 2014

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Identification of enriched PTM crosstalk motifs from large-scale experimental data sets.
Mao Peng, Arjen Scholten, Albert J R Heck, Bas van Breukelen

J Proteome Res· January 2014

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Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis.
Teck Yew Low, Sebastiaan van Heesch, Henk van den Toorn, Piero Giansanti, Alba Cristobal, Bas van Breukelen

Cell Rep· December 2013

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The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Richard G Côté, Johannes Griss, José A Dianes, Rui Wang, James C Wright, Bas van Breukelen

Mol Cell Proteomics· December 2012

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High confidence and sensitivity four-dimensional fractionation for human plasma proteome analysis.
Renato Millioni, Serena Tolin, Gian Paolo Fadini, Marco Falda, Bas van Breukelen

Amino Acids· November 2012

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Deep proteome profiling of circulating granulocytes reveals bactericidal/permeability-increasing protein as a biomarker for severe atherosclerotic coronary stenosis.
Onno B Bleijerveld, Patrick Wijten, Salvatore Cappadona, Elizabeth A McClellan, Ayse N Polat, Bas van Breukelen

J Proteome Res· November 2012

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Current challenges in software solutions for mass spectrometry-based quantitative proteomics.
Salvatore Cappadona, Peter R Baker, Pedro R Cutillas, Albert J R Heck, Bas van Breukelen

Amino Acids· September 2012

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Protease bias in absolute protein quantitation.
Mao Peng, Nadia Taouatas, Salvatore Cappadona, Bas van Breukelen, Shabaz Mohammed

Nat Methods· May 2012

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Database independent proteomics analysis of the ostrich and human proteome.
A F Maarten Altelaar, Danny Navarro, Jos Boekhorst, Bas van Breukelen, Berend Snel

Proc Natl Acad Sci U S A· January 2012

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Evaluating experimental bias and completeness in comparative phosphoproteomics analysis.
Jos Boekhorst, Paul J Boersema, Bastiaan B J Tops, Bas van Breukelen, Albert J R Heck

PLoS One· December 2011

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Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides.
Salvatore Cappadona, Javier Muñoz, Wim P E Spee, Teck Y Low, Shabaz Mohammed, Bas van Breukelen

J Proteomics· September 2011

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Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra.
Erik L de Graaf, A F Maarten Altelaar, Bas van Breukelen, Shabaz Mohammed, Albert J R Heck

J Proteome Res· September 2011

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A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data.
Isthiaq Ahmad, Frank Suits, Berend Hoekman, Morris A Swertz, Heorhiy Byelas, Bas van Breukelen

Bioinformatics· April 2011

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RockerBox: analysis and filtering of massive proteomics search results.
Henk W P van den Toorn, Javier Muñoz, Shabaz Mohammed, Reinout Raijmakers, Albert J R Heck, Bas van Breukelen

J Proteome Res· March 2011

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Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.
Andreas O Helbig, Sara Rosati, Pim W W M Pijnappel, Bas van Breukelen, Marc H T H Timmers

BMC Genomics· December 2010

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LysNDeNovo: an algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation.
Bas van Breukelen, Alexandros Georgiou, Madalina M Drugan, Nadia Taouatas, Shabaz Mohammed

Proteomics· March 2010

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