The latest addition to the PCF. The new timsTOF Ultra MS from Bruker was just upgraded to the Ultra 2 version. With its Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation Serial Fragmentation (PASEF) capabilites, it allows a much more efficient usage of peptide ions, giving this instrument unprecddented sensitivity and speed. It is therefore our prefered system for complex and low input samples. It is connected to a Vaquish Neo NanoLC system for high performance peptide separation that can run at a 30, 45 or 60 samples per day (SPD) setup.

The Orbitrap Eclipse Tribrid with UltraViolet PhotoDissociation (UVPD), Real-Time Searching (RTS) and High-field Asymmetric-waveform Ion-Mobility Spectrometry (FAIMS) is our prefered system for the precise quantification of complex samples using Tandem Mass Tags (TMT). With its multistage fragmentation capabilites and high sensitivity it is also ideally suited for the identification of cross-linked peptides. The Eclipse is connected to an Ultimate 3000 nano LC system. 

The two Thermo Orbitrap Exploris 480 are our workhorses for all Data-Independent Acquisition (DIA) workflows, like global SWATH-MS and targeted Parallel Reaction Monitoring (PRM)-MS analysis. One of the systems is connected to a Vanquish Neo LC with its excellent separation performance. The other is coupled to a EvoSep One LC. This LC is ideal for fast and robust analysis of large sample numbers (100+).

The Thermo Orbitrap Fusion Lumos Tribrid with Electron Transfer Dissociation (ETD) is connected to a EasyLC 1200 nano LC. As the Eclispe, it allows multistage fragmentation in the linear ion trap and also has a high-Field Asymmetric-waveform Ion Mobility Spectrometry (FAIMS) device. It is therefore ideally suited for the analysis of cross-linked peptides as well as for Label-Free Quantification (LFQ) workflows in (more traditional) Data-Dependent Acquisition (DDA) mode.