Equipment

KingFisher

The Kingfisher is a versatile benchtop instrument for automated magnetic bead-based sample processing of 96 samples per run; Compatible sample voluminal: 20-200 microliter; We use it primarily for automated EV capture using SAX beads from biofluids.

Bravo

The Agilent Bravo is a flexible liquid handling platform that can process up to 96 samples: we primarily use it for automated phosphopeptide capture using IMAC beads and Evotip loading

Ultimate3000

Online C18 reverse phase chromatography directly coupled to the mass spectrometer

EvoSep

Online C18 reverse phase chromatography directly coupled to the mass spectrometer

Qexactive HF

High-resolution mass spectrometer, equipped with advanced quadrupole technology and high-resolution Orbitrap; Fragmentation of precursor ions using HCD; Data acquisition in DDA and DIA mode

TimsTOF-HT

High resolution highthroughput mass spectrometer with ion mobility, for high dynamic range and analytical depth in quantitative proteomics; Data acquisition in DDA and DIA mode

After shot-gun data acquisition by nanoLC-MS/MS, raw data are processed by the software tool MaxQuant for peptide/protein identification and quantification. For DIA-MS data we use DIA-NN/Spectronaut, often in conjunction with dedicated libraries. Data exports to Excel are used for further dedicated statistical analyses, which is also facilitated by the OPL.

The computer infrastructure to cope with the large data flows is regularly upgraded. Currently, computing servers with > 100 CPU cores are connected to the tandem MS data acquisition PCs for fast data processing.

Storage servers provide hundreds of TB of local, temporary storage. These servers are connected to the VUmc store4ever system for long term archive, as well as Amsterdam UMC HPC and the national computing grid for additional computing power.