The facility is well equipped for biomolecule separations, proteomics and supportive biochemistry, and molecular biology.

For biomolecule separation, we have several gas chromatography and liquid chromatography systems that are off-line or on-line with mass spectrometers. The liquid chromatography systems provide excellent fractionation of mixtures proteins and peptides and facilitate downstream proteomic analyses.

A major component of protein separation work is carried out with 2D gel electrophoresis.  Here, the initial protein separation is done through isoelectric focusing (IEF) using the BioRad Protean IEF Cell or IPGphor from Amersham Biosciences.  Proteins are then separated by molecular mass using Criterion/Criterion Dodeca Cell from BioRad or Ettan Daltsix system from Amersham Biosciences. The resulting 2D gels can be stained with Coomassie, Silver and Sypro Ruby (all of which are compatible with mass spectrometric analysis).

High quality gel images are acquired with an Epson Expression 1640XLGA scanner for Coomassie and Silver stained gels, and a Typhoon 9410 imager (Amersham Biosciences) for Sypro stained gels. Gel images are then analyzed using Phoretix 2D Evolution gel analysis software (Nonlinear Dynamics Ltd.).

Following image analysis, interesting proteins are excised from gels by GelPix (Genetix Inc.) and digested by an automated digester, the MultiProbe II workstation (PerkinElmer Inc.). An aliquot of the protein digest is spotted onto a MALDI target plate by Multiprobe II workstation or Symbiot spotter (Applied Biosystems) and analyzed by a Voyager-DE STR MALDI-TOF mass spectrometer (Applied Biosystems). The acquired data are automatically submitted to database searching and protein identification by Proteomics Solution 1 (PS1) software (Applied Biosystems) or MASCOT v2.2 database searching engine.

If further mass spectral analysis is needed, the peptides can be directly sequenced using the oMALDI source of the QTOF XL Q-TOF mass spectrometer (Applied Biosystems) or separated by nano-flow LC (LC Packings or Eksigent) on the front end of the ESI (electrospray ionization) source of the Q-TOF MS/MS system.  Additionally, we have a 4000 Q-TRAP LC/MS/MS system (Applied Biosystems), which is a hybrid triple quadrupole/linear ion trap mass spectrometer ideal for drug discovery and development, metabolite identification and proteomic applications including post-translationally modified proteins discovery and biomarker validation.  

Automation of many of the steps in the above-described process enables us to work in a high throughput and efficient manner.  Furthermore, a Biacore 2000 system (Biacore Inc.) is available for studying protein interactions and the chip can also be analyzed using MALDI-TOF to identify protein complexes.

• EI and CI source

• Ion Trap analyzer with Full Scan, Selected Ion Monitoring and MSn capability

• Autosampler

• Multiple column mode.

• UV/VIS detector.

• PH meter.

• Conductivity cell.

• Semi-preparative flow cell.

• Fraction collector.

• Various sample inlet systems.

• Autosampler

• Diode Array Detector

• UV/VIS Detector

• Fluorescent Detector

•  reliable, high quality chromatographic separations produced up to 10 times faster than current HPLC methods, reducing time and cost per sample.

• increased efficiency for sharper peaks and better resolution, resulting in better quantitative and qualitative analyses.

• low dispersion, which yields up to a 5x increase in sensitivity.

• a variety of sample format options, from vials to plates, with the capacity to automate and hold waiting samples in a temperature-controlled environment.

• Famos Microautosampler

• UltiMate Micropump

• UV detector

• Switchos II Microcolumn Swithing Unit

• First dimension isoelectric focusing unit

• Take different immobilized pH gradient (IPG) strips

• Built-in power supply and cooling unit

• Second dimension gel separation unit

• Runs 13.3 cm x 8.7 cm gels

• Large variety of precast gels

• Two to four gel capacity (Criterion Cell)

• Twelve gels simultaneously (Dodeca Cell)

• Second dimension gel separation unit

• Runs 25.5cm x 20 cm gels

• High loading capacity

• Higher resolution

• Six gels simultaneously

• AutoFocus optics

• 1,600 x 3,200 dpi

• 42-bit colour and 16-bit grey

• 12.2 x 17.2 inch scan area

• FireWire

• High sensitivity and resolution

• 5-orders of magnitude dynamic range

• Various imaging modes:
  *PhosphorImaging
  *Blue excited fluorescence
    (457 nm and 488 nm)
  *Green excited fluorescence 532 nm
  *Red excite fluorescence 633 nm
  *Chemiluminescence

• Used for SyproRuby gels and DIGE gels

• Automated spot detection, matching and reliable image warping

• Flexible data display including 2D and 3D animation

• Batch process multiple analyses for high throughput

• MW/pI determination using standards

• Accurate densitometry and stastic quantitation

• Cross-stain analysis for Differential Gel Electrophoresis (DIGE) experiments

• XML import/export of data

• 8-channel excision head, 10 spots per minute

• Captures both visible and fluorescent images

• Cooled CCD camera, 16-bit Tif format

• 15 x 96 well plates, walkway automation

• 4 pin head

• Automated protein in-gel or in-solution digestion

• 2x 96 well plate

• User friendly methods

• Zip tipping and spotting

• Able to dissolve/dilute sample from microtiter plate and spot it onto MALDI target.

• Usage of ZipTips for sample purification possible.

• Positive and Negative ion mode.

• Linear and reflectron mode.

• PSD capable (Post Source Decay).

• CID cell (Collision induced dissociation).

• MALDI, Electrospray, and Nanospray source.

• Ultimate LC unit for 1- and 2D on-line chromatography

• Positive and Negative ion mode.

• CID cell (Collision induced dissociation).

• Enables high-sensitivity full-scan MS, MS/MS, and MS3 with high-selectivity from true triple quadrupole precursor ion (PI) and neutral loss (NL) scans.

• Perform multiple reaction monitoring (MRM) for quantitation using high-sensitivity triple quadrupole.

• Identify, characterize, and quantitate metabolites more quickly and easily.

•  Identify and sequence post-translationally modified (PTM) peptides automatically in a single LC/MS/MS run.

• Facilitates hypothesis-driven biomarker discovery and validation.

• 4 flow cells per chip allow two experiments including controls

• Autosampler with temperature control (4-40ºC)

• Affinity studies

• Kinetics

• Determination of valences

• Bound analytes can be eluted for subsequent MS analyses

• Batch and Real-time database searching

• AutoMS-Fit

• PS1 Conversion Utilities

• SymBiot Automation

• Multi database searches

• A powerful database search engine

• Integrates all the proven methods of database searching

• Peptide Fingerprint, Sequence Query and MS/MS Ion Search

• Unique, true probability-based scoring

• Total flexibility in chemical/post-translational modifications

• Batch or Real-time mode

• Use any nucleic or amino acid database in FASTA format