Bas van Breukelen – Bioinformatic tools for Proteomics

13 Mar Bas van Breukelen – Bioinformatic tools for Proteomics

Bas van Breukelen focuses on the analysis of data originating from proteomic experiments. Bioinformatics tools are developed to identify and quantify proteins presents in those very large datasets. In addition software and algorithms are developed that aid statistical analysis and data visualization.

Highlighted publications

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• Smit MA1, Maddalo G2, Greig K1, Raaijmakers LM3, Possik PA1, van Breukelen B3, Cappadona S3, Heck AJ3, Altelaar AF4, Peeper DS5. ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma. Mol Syst Biol. 2014 Dec 23;10:772. PMID: 25538140. [PubMed] [Read by QxMD] Treatment of BRAF mutant melanomas with specific BRAF inhibitors leads to tumor remission. However, most patients eventually relapse due to drug resistance. Therefore, we designed an integrated strategy using (phospho)proteomic and functional genomic platforms to identify drug targets whose inhibition sensitizes melanoma cells to BRAF inhibition. We found many proteins to be induced upon PLX4720 (BRAF inhibitor) treatment that are known to be inv [...]
• Binai NA1, Bisschops MM, van Breukelen B, Mohammed S, Loeff L, Pronk JT, Heck AJ, Daran-Lapujade P, Slijper M. Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures. J Proteome Res. 2014 Aug 1;13(8):3542-53. PMID: 25000127. [PubMed] [Read by QxMD] Stationary-phase, carbon-starved shake-flask cultures of Saccharomyces cerevisiae are popular models for studying eukaryotic chronological aging. However, their nutrient-starved physiological status differs substantially from that of postmitotic metazoan cells. Retentostat cultures offer an attractive alternative model system in which yeast cells, maintained under continuous calorie restriction, hardly divide but retain high metabolic activity an [...]
• Liu F1, van Breukelen B1, Heck AJ2. Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS. Mol Cell Proteomics. 2014 Oct;13(10):2776-86. PMID: 24980484. [PubMed] [Read by QxMD] Disulfide bond identification is important for a detailed understanding of protein structures, which directly affect their biological functions. Here we describe an integrated workflow for the fast and accurate identification of authentic protein disulfide bridges. This novel workflow incorporates acidic proteolytic digestion using pepsin to eliminate undesirable disulfide reshuffling during sample preparation and a novel search engine, SlinkS, t [...]
• Walzer M1, Pernas LE2, Nasso S3, Bittremieux W4, Nahnsen S1, Kelchtermans P5, Pichler P6, van den Toorn HW7, Staes A8, Vandenbussche J8, Mazanek M6, Taus T6, Scheltema RA9, Kelstrup CD10, Gatto L11, van Breukelen B7, Aiche S12, Valkenborg D13, Laukens K4, Lilley KS14, Olsen JV10, Heck AJ7, Mechtler K6, Aebersold R15, Gevaert K8, Vizcaíno JA16, Hermjakob H16, Kohlbacher O1, Martens L17. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics. 2014 Aug;13(8):1905-13. PMID: 24760958. [PubMed] [Read by QxMD] Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles [...]
• Guerreiro AC1, Benevento M1, Lehmann R2, van Breukelen B1, Post H1, Giansanti P1, Maarten Altelaar AF3, Axmann IM4, Heck AJ3. Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins. Mol Cell Proteomics. 2014 Aug;13(8):2042-55. PMID: 24677030. [PubMed] [Read by QxMD] Circadian rhythms are self-sustained and adjustable cycles, typically entrained with light/dark and/or temperature cycles. These rhythms are present in animals, plants, fungi, and several bacteria. The central mechanism behind these "pacemakers" and the connection to the circadian regulated pathways are still poorly understood. The circadian rhythm of the cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus) is highly robust and controll [...]

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