Sample Preparation

PreOmics tools

The BeatBox for tissue homogenization and cell lysis, and PreOn for automated sample preparation were installed in June 2023. The BeatBox can process up to 96 samples between 1-50 mg simultaneously with complete homogenization in as little as 10 minutes. The PreOn can accommodate up to 12 samples to fully prepare proteomics samples in as little as 3 hours from homogenates or lysates to peptides for LC-MS/MS analysis.

Thermo Vanquish Flex UHPLC with fraction collection

The Vanquish Flex was installed in March 2023 to further enhance the capabilities of the Mass Spectrometry and Proteomics Core facility. This instrument is controlled by Chromeleon 7.3 software, has a quaternary pump, UV detector, fraction collector, and can accommodate a wide range of column chemistries to separate biomolecules.

Other equipment:

• SpeedVac SPD120 vacuum concentrator
• Sorvall Legend RT benchtop centrifuge capable of holding 15 mL tubes and 96-well plates

Mass Spectrometers

Thermo Orbitrap Fusion Lumos

The Lumos was installed in May 2017 and is equipped with a Vanquish Neo nano-UPLC coupled to the mass spectrometer through a nano-electrospray ionization source. This instrument has multiple fragmentation capabilities with both high-resolution (Orbitrap) and low-resolution (Ion Trap) mass analyzers.

Thermo Orbitrap Ascend

The Ascend was installed in March 2023 and is equipped with a Vanquish Neo nano-UPLC interfaced through a nano-electrospray ionization source. This instrument has multiple fragmentation capabilities with both high-resolution (Orbitrap) and low-resolution (Ion Trap) mass analyzers. In addition, the Ascend has a high Field Asymmetric waveform Ion Mobility Source (FAIMS) which sorts the ions at the orifice, which helps improve the sensitivity and selectivity of desired ions. This instrument is also equipped with real-time searching capabilities.

Bruker timsTOF HT

The timsTOF HT was installed in June 2023 and is equipped with either a nanoElute 2 nano-flow UPLC for proteomics applications and an Elute for high-flow applications such as metabolomics and lipidomics, respectively. This instrument has an added dimension of separation – ion mobility – to further interrogate proteome depth by data-independent acquisition and separate isomers unresolved in the LC or MS dimension. Real-time searching via PASEF technologies improves throughput and detection from empirically or library-free generated spectral libraries.

Data Analysis

The Mass Spectrometry and Proteomics Core has three permanent licenses to Proteome Discoverer for proteomics data analysis from the Thermo systems, including permanent licenses for Chymeris and XlinkX. Analysis for proteomics datasets collected on the Bruker timsTOF HT are searched in real-time with PASEF and untargeted metabolomics and lipidomics datasets can be analyzed on one of two stand-alone data analysis systems dedicated to these workflows.