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Rockefeller University

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 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 ETD as well as MSn fragmentation experiments.
  • Q-Exactive HF (donated by the Leona M. and Harry B. Helmsley Charitable Trust) is operated in nano-flow mode (Dionex 3000) and is dedicated to proteomics.
  • Orbitrap XL is dedicated to higher flow LC and the analysis of small molecules, metabolites, nucleoside’s or for example when high mass accuracy and/or MS/MS is needed for molecules and larger amounts are available.
  • Q-Exactive Plus (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 operated in higher microliter-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.
  • GC-MS (Agilent 5977B Inert Plus MSD w/Intuvo 9000 GC) with a Gerstel sampler (MPS-xt).
  • 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)

 

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). Data viewer is available.
  • Skyline – for targeted analysis.
  • Spectronaut – search engine to query Data Independent Acquisition (DIA) data (commercial). Data viewer is available by request to vendor (support@biognosys.com).
  • Compound Discoverer – for data dependent metabolomics analysis (commercial)
  • Perseus – for data analysis

 

 

Internal Rockefeller users can access pLIMS sample information, progress, and final invoices using the link below.
Sample Status

Contact

The Rockefeller University
The Proteomics Resource Center, Box 105
1230 York Avenue
New York, NY 10065-6399