Services

Submission Dates

Gel bands for protein ID are typically processed once each month. Please submit your samples during the following weeks, from 10.00-11.00 am and 2.00-3.00pm. Samples dropped off after these dates will be stored and processed on the following month:

    2019:    Nov 4-8
   
    2020:    Jan 6-10
                Feb 3-7
                Mar 2-6
                Apr 6-10
                May 4-8
                Jun 1-5

All other samples are received from Monday to Friday from 10.00-11.00 am and 2.00-3.00pm. Please contact bms@dal.ca to arrange a sample delivery date.

Protein Identification

Proteins isolated in SDS-PAGE gel bands or in solution are can be identified using ‘bottom-up’ techniques. Samples are digested in our fully automated Progest Station, and analyzed by ESI-LC-MS/MS on a high resolution VelosPRO Orbitrap system. The MS data is processed using Proteome Discoverer/SEQUEST software and proteins hits are reported in user friendly Excel files.

Please give a short notice of your samples to: bms@dal.ca or call 902-494-8359. For details on gel staining, storage and handling conditions, see FAQs.

For in-solution analyses, please contact bms@dal.ca or call 902-494-8359 to consult buffer compatibility, pricing and arrange sample drop-off.

Intact Protein Analysis

Intact molecular weights of proteins up to 500KDa can be determined by infusion/electrospray ionization (ESI-MS) on our VelosPRO Orbitrap system in combination with spectral deconvolution software (BioAnalyst). Proteins need to be purified and resuspended in a MS compatible buffer.

Please contact bms@dal.ca or call 902-494-8359 for further information and arrange sample drop-off.

Quantitative Profiling

The BMS Lab accepts proteins extracted from biological samples, such as cells, tissues and blood for quantitative proteomic analyses. These experiments provide identification and relative abundances for hundreds and even thousands of proteins expressed in variable experimental conditions.

Discovery Proteomics: We perform both labeled (TMT, iTRAQ, SILAC, reductive dimethylation, ICAT) and label-free quantitation in conjunctions with 1D and 2D liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) on our VelosPRO Orbitrap system. The data obtained from these experiments are distilled with bioinformatic tools that transform the complex LC-MS/MS files into clear and biologically meaningful datasets which can be easily interpreted by researchers.

Targeted Proteomics: Known or hypothetical proteins can be specifically targeted for quantification using Selected Reaction Monitoring (SRM, also known as Multiple Reaction Monitoring or MRM) mode acquisitions on our QTrap 5500 LC-MS/MS system. This approach offers enhanced sensitivity and can be used to profile hundreds of proteins in a single run. Data is analyzed using Skyline, a publicly available software for SRM based experiments.

Both Discovery and Targeted experiments are time and labour intensive. The success of these approaches relies on detailed planning and choosing the appropriate sample preparation techniques.

Please contact bms@dal.ca or call 902-494-8359 to consult which approach is compatible with for your research. Pricing and scheduling will vary according to the complexity of analyses.

Post-Translational Modifications

The state-of-the-art MS/MS systems in our lab can be tuned and optimized to obtain further structural protein information such as single nucleotide polymorphisms and post-translational modifications. These techniques often require specific sample enrichment steps and custom developed MS-MS methods. For example, analysis of phosphorylated proteins often requires an IMAC or TiO2 enrichment methods combined with Precursor Ion/Neutral loss MS/MS scans.

Please contact bms@dal.ca or call 902-494-8359 to consult whether these experiments can be applied to your research.

Metabolomics/Small Molecules

The Biological Mass Spectrometry Core Facility at Dalhousie University is equipped with versatile tandem mass spectrometry systems that can be tuned and optimized for the identification and quantification of biologically important molecules such as drugs, metabolites, lipids, sugars, nucleic acids, hormones and vitamins.

These analyses are done using targeted or non-targeted (discovery) approaches. Targeted analyses are done by liquid chromatography (Ulimate 3000, ThermoScientific or Agilent 1100 LC systems) coupled to a triple quadrupole/linear ion trap tandem mass spectrometer (Qtrap5500, Sciex) operated in Selected Reaction Monitoring (SRM, aka Multiple Reaction Monitoring, MRM) mode. Additinal specificity and sensitivity can be achieved using the differential ion mobility source (Selexion).

Data analysis is done using vendor-neutral Skyline software platform. We based our methods on the Asara et al (Nature Protocols, 2012 7(5): 872-881) publication, and currently targeting approximately 300 metabolites of major metabolic pathways. [PDF - 44KB] The list is currently being expanded to include other compounds.

Non-targeted or discovery of metabolites/unknown compounds is performed by liquid chromatography (Vanquish UHPLC system, ThermoScientific) coupled to a high resolution quadrupole-orbitrap tandem mass spectrometer (QExactive, ThermoScientific). MS and MS/MS data is acquired using data-dependent acquisition mode. Metabolites/unknown compounds are identified and quantified using MS1 and MS2 databases on Compound Discoverer 2.2 software (ThermoScientific).

Please contact bms@dal.ca or call 902-494-8359 to consult for custom-made MS analyses for your compounds of interest.

Lipidomics

The Biological Mass Spectrometry Core Facility at Dalhousie University can perform lipid profiing on its UHPLC-MS/MS (Thermo Vanquish LC-QExactive MS/MS) system. Data is analyzed and processed using LipidSearch software, allowing the identification and quantification of the diverse and complex lipid spectra.

Please contact bms@dal.ca or call 902-494-8359 to consult for custom-made MS analyses for your compounds of interest.

Custom Analysis

Please contact bms@dal.ca or call 902-494-8359 to consult for custom-made MS analyses for your compounds of interest.