Instruments and Software used at the Proteomics Resource Center
The Proteomics Resource Center are equipped with a variety of LC and MS systems, including GC-MS and MALDI, and also houses peptide synthesizers.
- Fusion Lumos(opens in new window) 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 mode and the setup is currently dedicated to proteomics. The Fusion Lumos allows for CID, HCD and Electron Transfer Dissociation (ETD) as well as MSn fragmentation experiments.
- Q-Exactive HF(opens in new window) (donated by the Leona M. and Harry B. Helmsley Charitable Trust) is operated in nano-flow mode (Dionex 3000) and is dedicated to proteomics.
- Q-Exactive Plus(opens in new window) (sponsored by the Leona M. and Harry B. Helmsley Charitable Trust) operated in higher microliter-flow-mode (Vanquish HPLC) and is dedicated to metabolomics.
- IQ-X Orbitrap(opens in new window) operated in higher microliter-flow-mode (Vanquish HPLC) and is dedicated to metabolomics.
- Fusion Ascend(opens in new window) w/ETD and Proton Transfer Charge Reduction (PTCR). This instrument is operated with nano-flow LC and is currently dedicated to proteomics. The Fusion Lumos allows for CID, HCD and ETD as well as MSn fragmentation experiments.
- GC-MS (Agilent 5977B Inert Plus MSD w/Intuvo 9000 GC) with a Gerstel sampler (MPS-xt).
- Typhoon 9400 Variable Mode Laser Scanner (click for usages fee and policy for use)
Software’s: To answer the many types of questions that can be asked the Center operates many different software’s.
- Proteome Discoverer(opens in new window) – used together with MASCOT and/or SEQUEST and other node based tools (commercial)
- Mascot(opens in new window) – search algorithm (commercial)
- Sequest– search algorithm (commercial)
- MaxQuant(opens in new window) – search algorithm with quantitation.
- PEAKS(opens in new window) – Denovo based search algorithm (commercial). Data viewer is available(opens in new window).
- Skyline(opens in new window) – for targeted analysis.
- LipidSearch(opens in new window) – search algorithm (commercial) for Data Dependent Acquisition based analysis of lipids.
- Spectronaut(opens in new window) – search engine to query Data Independent Acquisition (DIA)(opens in new window) data (commercial). Data viewer is available by request to vendor (support@biognosys.com(opens in new window)).
- Compound Discoverer(opens in new window) – for data dependent metabolomics analysis (commercial)
- Perseus(opens in new window) – for data analysis