Instruments and Software used at the Proteomics Resource Center
Mass spectrometers: The Proteomics Resource Center are equipped with a variety of LC-MS systems and also houses a GC-MS and a MALDI mass spectrometer.
- Fusion Lumos w/APD. The Fusion Lumos was sponsored by the Sohn Conference Foundation. The instrument is connected to a 1200 Easy LC operating in nano-flow and the setup is currently dedicated to proteomics. The Fusion Lumos allows for CID, HCD and ETD as well as MSn fragmentation experiments.
- Q-Exactive HF (donated by the Helmsley Foundation) is operated in nano-flow (Dionex 3000) and is also dedicated to proteomics.
- Orbitrap XL is dedicated to higher flow LC and the analysis of small molecules, metabolites, nucleosides or for example when high mass accuracy and/or MS/MS is needed for molecules and larger amounts are available.
- Q-Exactive Plus operated in higher uL-flow-mode (Vanquish HPLC) and is dedicated to metabolomics.
- Our Vantage triple quadrupole is operated in high flow and used for example for MRM based analysis of nucleosides.
- An LTQ linear ion trap is used for quality control of synthesized peptides.
- MALDI (STR Voyager) is available as a walk-up/user instrument.
- GC-MS (Agilent 5977B Inert Plus MSD w/Intuvo 9000 GC).
- Off-line LC based fractionation setup with UV or MS detection.
- Typhoon 9400 Variable Mode Laser Scanner (click for usages fee and policy for use)
- Rainin Peptide Synthesizer by Protein Technologies.
- Intavis LLC Peptide Synthesizer by Protein Technologies.
Software’s: To answer the many types of questions that can be asked the Center operates many different software’s.
- Proteome Discoverer – used together with MASCOT and/or SEQUEST and other node based tools.
- Mascot – search algorithm (commercial)
- Sequest– search algorithm (commercial)
- MaxQuant – search algorithm with quantitation.
- BYonic – search algorithm with quantitation (commercial)
- PEAKS – Denovo based search algorithm (commercial)
- Skyline – for targeted analysis
- Compound Discoverer – for data dependent metabolomics analysis (commercial)
- Perseus – for data analysis