Equipment

LTQ Velos Orbitrap with ETD

LTQ Velos Orbitrap with ETD

Ideal for identifying low abundance proteins and characterizing protein post-translational modifications. 

  • Superior Sensitivity at the sub-femtomole (< 10-15 moles) level
  • ETD (Electron transfer dissociation) — especially valuable for characterizing protein post-translational modifications
  • Front End: a dedicated Eksigent NanoLC-Ultra and NanoFlex ChipLC system
  • Non-splitting flow control
  • Outstanding reproducibility
  • Outstanding mass accuracy (routinely 1-2 ppm) and resolution (up to 100,000)
  • Microfluidic chips as columns
orbitrap machine
orbitrap machine wide view

TSQ Vantage Triple Quadrupole Mass Spec

TSQ Vantage Triple Quadrupole Mass Spectrometer

Workhorse of quantifying proteins, peptides and metabolites. i.e. biomarker validation and pharmacokinetics.

  • Linear dynamic range of four orders of magnitude for quantitation (0.01fmol-100fmol)
  • Multiple scanning modes: High-sensitivity full-scan, Selected Ion Monitoring (SIM), Selected Reaction Monitoring (SRM) and others
  • Quantitation-Enhanced Data-Dependent MS/MS (QED-MS/MS) for simultaneous compound confirmation and quantitation
  • Versatile HPLC front end:
    • Conventional flow with Shimadzu HPLC and electrospray (HESI-II) source
    • Capillary and Nano-flow with Eksigent HPLC and nanospray source
triple quad mass spec

Typhoon 9500

Typhoon 9500 Phosphorimager/Scanner

The core facility has an Amersham Typhoon 9500 Phosphorimager/Fluorescence Scanner. This versatile system will image gel sandwiches, gels, membranes, microplates, and even microarrays, and it provides high sensitivity detection and quantitation of fluorescent stains and probes used for gel analyses of proteins as well as more traditional immunobloting procedures. Automated four-color fluorescence scanning allows multiplexing of multiple targets in the same sample, ensuring accuracy of analysis, increasing throughput, and saving time. This system can be used with the DIGE (Difference Gel Electrophoresis) methodology which uses amine-directed cyanine-based dyes (Cy-Dyes) to label proteins for differential quantitation on a single gel. 

Typhoon 9500 Phosphorimager

emission filters

Emission Filters Available:

Filter Type Wavelength Range (nm) Detection Examples
In the machine:
IP BP390 Phosphorimaging
LPB (510LP) ≥510 Cy2, SYBR Green, FAM, FITC, Alexa Fluor 488, Sypro Ruby, Sypro Orange, GFP
LPG (575LP) ≥575 Cy3, Deep Purple, HEX, Alexa Fluor 532 and 555, Sypro Red
LPR (655LP) ≥665 Cy5, Alexa Fluor 633, TOTO 3, DiD, Cy5 DIGE Fluor, ECL Plex Cy5
Not currently in the machine, but available:
BPB1 (530DF20) 520-540 Cy2 DIGE Fluor, ECL Plex Cy2
BPG1 (570DF20) 560-580 Cy3 DIGE Fluor, ECL Plex Cy3

 

PDQuest Gel Analysis

PDQuest Gel Analysis Software

The core facility has a site license for the Bio-Rad gel analysis software PDQuest. This imaging software helps to align multiple gels and to organize the array of spots so that each spot can be individually analyzed. There is also a vertical and horizontal streak reduction routine. 3D data (X-, Y- position and fluorescence intensity) can be used to calculate a volume for each spot that can be used to quantify the amount of protein in the spot and to compare it to other spots. The spot’s volume can be normalized to the total spot intensities to take into account loading variation. This allows spots to be compared on different gels. Once normalized, data from several gels can be averaged and used to generate statistically significant databases of spot volume and, therefore, amount of protein in the spot. These databases can then be compared to detect differences in protein levels in specific spots, so this approach is a visual method of expression difference quantitation.