Beckman Optima MAX Ultracentrifuge

The Beckman Optima MAX Ultracentrifuge is capable of reaching speeds up to 130,000 rpm (1,019,000 x g). This machine is ideal for the pelleting of small particles that include viruses and subcellular organelles. The removal of these particles is of particular interest when running the AKTA FPLC as these small particles could interfere with column binding.

Available Rotors:

MLS 50 Swinging-Bucket Rotor
MLA 80 Fixed Angle Rotor
MLA 130 Fixed Angle Rotor
TLN 100 Fixed Angle Rotor

Download ultracentrifuge protocol

PerkinElmer VICTOR 1420-40 Multilabel Counter

Victor 3 1420-040 multilabel counter is used for
fluorometry (including top counting and bottom counting), luminometry, photometry (including UV absorbance), TR-fluorometry (including LANCE), and fluorescence polarization.  The instrument also includes a 2-channel dispenser option.  The 2-channel liquid injector allows for an addition of a reagent to start or terminate a process (e.g. an enzyme reaction).

The Victor multilabel counter is equipped with the following filters:
CW-lamp filters: 560, 570, 595, F355, F485, P405, P450 and P490;
Emission filters: D545, D572, D615, D642, D665, F460 and F533;
(F-fluorometry, P-photometry (absorption), D-time-resolved fluorormetry and Lance filter).

Wallac 1420 (version 3.00) software is used to control the system, however, the results can be exported to an excel file for further data analysis.

Note: the size of the plate used for Victor should be less than 8.7 cm X 12.8 cm.

LI-COR Biosciences Odyssey

Odyssey from LI-COR Biosciences is an infrared imaging system that uses two independent infrared fluorescent channels (700 nm and 800 nm) for detection, enabling simultaneous two-colour target analysis.

Odyssey offers a wide range of applications:

• Western blots including two colour blots and in-gel westerns
• Protein detection including traditional colloidal Coomassie stained gel and protein arrays
• Cell-based assays including in-cell and on-cell westerns
• Nucleic Acids assays including EMSA/Gel Shift and DNA Staining
• Tissue imaging
• Microwell assays including ELISA/FLISA Transcription Factors

Odyssey application software uses a variety of familiar tools for analyzing image files created on the Odyssey imager. The core application includes scan control, band sizing, quantification, project management, and reporting. The image can be exported to individual image file (.tif or .jpeg file).

Amersham AKTA Purifier FPLC System

ÄKTA™ FPLC™ is a biocompatible, large scale sample preparation system capable of ion exchange/size exclusion/affinity/hydrophilic interaction/reversed phase chromatography. The ÄKTA purifier 10, housed in the FPF, is equipped with the following components: P-903 Pump (10 ml pump with a flow rate range of 0.001-10 ml/min and a pressure range of 0-25 MPa), UV-900 Detector (3 wavelength settings), pH/C-900 Monitor (pH and conductivity measurement during LC), and Frac-900/901 Fraction Collector (automated collection of up to 175 fractions).

ÄKTA FPLC is controlled by UNICORN™ software. Pre-programmed templates support all the methodology needed for high performance.

Users must supply their own columns and prepare their own buffers. Subsequent to running the FPLC, users are responsible for replacing their column with bypass tube and cleaning the system with 20% ethanol.

Download related protocols:

AKTA purifier Quick Start Protocol
Cleaning the AKTA system after usage

Gel Preparation Instrumentation

Ettan IPGphor II

Ettan IPGphor II Isoelectric Focusing System performs the first dimension of 2D gel electrophoresis, protein isoelectric focusing (IEF). This system can run up to 12 IPG strips from 7cm to 24 cm. The facility has both fixed and variable-length strip holders available for use.

Download 2D gel protocol.

BIO-RAD Protean Plus Dodeca Cell

The PROTEAN Plus Dodeca cell accommodates up to 12 large gels, matching the capacity of the first dimension runs in the Ettan IPGphor II system, for high-throughput 2D application. The PROTEAN Plus Dodeca System is equipped with cell cooling, recirculation, and plate electrodes. The handcasting system includes the PROTEAN Plus hinged spacer plates, PROTEAN Plus multi-casting chamber, and the Model 495 gradient former.

PROTEAN Plus Multi-Casting Chamber

The PROTEAN plus Multi-Casting Chamber allows for up to twelve gels (1.0, 1.5 or 2.0 mm in thickness) to be cast simultaneously for use in the PROTEAN plus Dodeca Cell. Monomer can be introduced from the top or the bottom to prepare identical linear gradients or single percentage gels. Cast gels can be stored up to 2 week at 4ºC.

Mini-PROTEAN Plus 3 Multi-Casting Chamber

The PROTEAN 3 Multi-Casting Chamber is used to cast as many as twelve gels (0.5-1.5 mm in thickness) simultaneously for use in the PROTEAN 3 cell and PROTEAN 3 Dodeca Cell. Cast gels can be stored up to 2 weeks at 4ºC.

BIO-RAD Mini-PROTEAN 3 Dodeca Cell

The BIO-RAD Mini-PROTEAN 3 Dodeca Cell is capable of running multiple polyacrylamide gels simultaneously (up to 12 handcast (8.3 x 7.3 cm) or precast (8.6 x 6.8 cm) gels. It is equipped with a built-in cooling coil attached to an external refrigerator circulator to prevent overheating and ensure reproducible, high-resolution results.  A stirbar maintains uniform buffer temperature.

BIO-RAD Criterion Dodeca Cell

Criterion Dodeca cell is used to run 1 to 12 Criterion gels simultaneously.

BIO-RAD PROTEAN Dodeca Stainer

Dodeca stainer is a high-throughput gel staining device that accommodates up to 12 (20 X 20.5 cm) gels.

The Dodeca stainer is compatible with Bio-Safe colloidal Coomassie Brilliant Blue G-250 stain, Coomassie Brilliant Blue R-250 stain, SYPRO Ruby protein gel stain, mass spectrometry compatible Dodeca Silver stain kit, and the original Silver stain kit (mass spectrometry incompatible).

The Silver stain plus kit is not compatible with this system.

Polyacrylamide Gel Staining protocols

Gel Imaging and Analysis

Epson Perfection 4990 Photo Scanner

Epson Perfection 4990 Photo scanner contains a built-in transparency unit with moving light source. It can scan gels up to 8.5" x 11.7" in size.

Download related Protocols:

ProXPRESS 2D Proteomics Imaging System

The ProXPRESS 2D Proteomic Imaging System is a UV/Visible transmission and fluorescence imager. It is capable of measurements on a variety of media including gels, microscope slides, tissue culture plates and exposed film. It has a maximum scanning area of 330 mm x 270 mm at resolutions of up to 33 microns. The 2D imaging system is equipped the following filter: excitation: 460/80, 480/30, 550/10 emission: 530/30, 650/150, 580/10 for fluorescence scan, as well as 2/0 for silver and coomassie scan.

Three illumination methods are normally used to generate images:

• Top: using a high power xenon light source with interference filters for fluorescence measurements. This function is used for fluorescent stained gels.
• Bottom: using a UV light source and UV-to-visible light converter plate for densitometry measurements. This method is used for silver and coomassie stained gels.
• None: no light source is utilized. This method is used for the Western Blot imaging as an alternative to using film.

After scanning, an image file in .tif format can be exported and analyzed with Progenesis SameSpots analysis software. A spot pick-list generated by Progenesis SameSpots can be used for Ettan Spot Picker.

GE Storm 820® Phosphorimager

The GE Storm™ 820® Phosphorimager performs autoradiography for nucleic acid and protein gel analysis. The Scan area can be as large as 35 × 43 cm.  The resultant images are analyzed using ImageQuant 5.2 software and can be exported to other programs in the tiff file format.

Key Parameters:
Screen compatibility: Storage Phosphor Screens Hard or Soft backed (3 Hard backed screens on site)
Image eraser is also available on site.

Download Storm 820 operation protocol

Progensis SameSpots

Progensis SameSpots is a 2D gel image analysis tool that allows for spot alignment at the pixel level, resulting in 100% matching across all gels in an experiment.  Once aligned, the user can assign treatment groups and define the gels area of interest.   Automatic analysis can be run with or without spot filtering, with the resulting spots of interest ranked according to p-value from one way ANOVA analysis, or by fold change based on normalized volume.  Spot images can then be viewed in either 2D or 3D montage windows for an even closer look.  Here, the user can decide which spots to further analyze with Progenesis Stats.  The software clusters the data at this step, giving the user an insight as to how proteins may be related, or to create or validate a hypothesis. 

The Progenesis SameSpots software is compatible with the Ettan™ Robotic Spot Picker.  This allows the user to generate a picklist for the excision of non visual spots.

Please note: To perform alignment in this application, a group of images in .tiff format is required.

Ettan™ Spot Picker

The Ettan™ Spot Picker is a robotic system designed to pick protein spots from 1D or 2D gels and transfer the picked gel spots into a 96 well microplate in preparation for automatic digestion.

Two functions are available:

Manual: protein spots are extracted from the gel visually by the use of a camera mounted on the spot picker. This method for spot isolation is only available for gels stained with dyes detectible under a visible light.

Automatic: the user can import a file containing the coordinates of the desired spots. This file is referred to as a Picklist, and is generated using the Progenesis SameSpots software. This function is available to gels that are fixed ('backed') onto a glass plate with reference markers attached to the glass surface.

The Ettan Spot Picker is capable of picking up to 384 plugs in any single picking run.

Ettan™ Spot Picker is supplied with 1.4-mm and 2.0-mm picker heads.

Download related Protocols:

How to use manual picking with Click N Pick
How to back gel
How to generate pick list by PG220
How to use automatic picking with pick-list

Waters MassPREP Station for Automated In-gel Digestion
(Operated by Facility staff only)

The Waters MassPREP Station is designed for the automated de-staining, reduction, alkylation, in-gel proteolytic digestion of proteins and extraction of peptides.  After extraction, peptide solutions are lyophylized for minimal sample loss.  The complete process takes 2 - 3 days.

The standard system in our facility allows two 96-well plates to be processed simultaneously.

The Waters MassPREP Station is designed for the automated de-staining, reduction, alkylation, in-gel proteolytic digestion of proteins and extraction of peptides.  After extraction, peptide solutions are lyophylized for minimal sample loss.  The complete process takes 2 - 3 days.

The standard system in our facility allows two 96-well plates to be processed simultaneously.

LC-MALDI Prep

This instrument has not yet been implemented. We will develop standard operating procedures for the LC-MALDI once the demand for this instrument arises.