Current instrumentation, methodologies and workflows

Equipment. Currently the following instruments are operational at the facility:

  • Electrospray Ion Trap Fourier Transform Ion Cyclotron Mass spectrometer (LTQ FT, ThermoFinnigan), equipped with nanoElectrospray source.
  • NEW!!! Orbitrap Fusion Lumos (ThermoFinnigan), equipped with nano electrospray source, conected to on-line uHPLC (EasynLC 1200)
  • Triple Quadrupole (Quantum AM ThermoFinnigan) equipped with nanoElectrospray source.
  • Automatic Gel Slicer, with gel documentation and DIGE capabilities (ProPicII, DIGILAB Genomic Solutions)
  • Automatic Digestor (ProGest, DIGILAB Genomic Solutions)

Search engines/computer software

  • Database search servers: SEQUEST Cluster, Proteome discorverer (version 2.2) and MaxQuant. The Sequest cluster is running on a dedicated 8 node double processor server. The proteome discoverer and MaxQuant are running on a 32 procesor workstation.
  • PEAKS (from Bioinformatics solutions). new software tool for protein identification and quantization, de novo peptide seqiuencing. To download a viewer click here.
  • HDExaminer (from Sierra Analytics) is now our prefer software for analysis of protein dynamics by HDX MS

Some of the tools used at our facility have been custom build:

  • HDXFinder (software for D/H Exchange analysis): A set of web-based computer applications for assisted Deuterium Exchange Mass Spectrometry Analyisis. Access to this portal is free to academic users. Optimized for Mozilla Firefox. A draft of the manual can be downloaded here. Programer: Danny Miller. A project in collaboration with A. Fenton:
  • SAIDE: a cooling chamber for DX MS experiments. This is an interface for HPLC and MS build by Mecour.
    • M.T. Villar, D. E. Miller, A.W. Fenton and A. Artigues: SAIDE: A Semi-Automated Interface for Hydrogen /Deuterium Exchange Mass Spectrometry (HDX MS). (2010) Proteomica 6:63-69.
  • AIDE: A fully automatic interface for HDX MS This new interface has two working modes: quench flow for subsecon to 30 second time scale and normal rate for reactions times above 30 sec.

Pressure cell ss

Our new cell is a combo, a shorter version of the SS that has a transparent insert that can be used for sample loading.

Last modified: Aug 22, 2017