In 2005 he joined the lab of Matthias Mann in Munich, Germany as a post-doctoral fellow. In 2009 he was appointed as assistant professor and in 2013 as associate professor at the University Medical Center Utrecht in The Netherlands. In February 2014 he was appointed as full professor at the Radboud University in Nijmegen, The Netherlands. Awarded grants include NWO-VIDI (2009), an ERC Starting Grant (2012) and an ERC Consolidator Grant (2017). Vermeulen is a leader in the proteomics field and his lab uses state-of-the-art quantitative mass-spectrometry-based proteomics technologies. The lab integrates conventional protein biochemistry, CRISPR/Cas9, genomic sequencing (ChIP-seq, RNA-seq DNAseI-seq) and imaging approaches.