Proteomics Core Facility

Overview:

To provide clinical and academic researchers access to proteomics technologies and expertise to solve their questions related to the identification, characterization, and quantification of proteins. This helps rese

Core service and technology:

The Proteomics Core Facility provides Mass Spectrometry (MS) based proteomic analyses service complemented by research personals with expertise in the field as well as state-of-the-art equipment with the latest cutting-edge technology capable of performing 4D proteomics.

To avail the services of the Proteomics Core, the interested researchers must submit the project details to the core facility lead. Once the project details have been reviewed by the Core team it will be forwarded to TRI management for scoring and approval.

Services available:

1. Sample pre-fractionation by in-gel or off-gel techniques
   In-gel fractionation performed using 1D SDS-PAGE and off-gel fractionation by strong cation exchange (SCX) fractionation technique.

2. Protein identification
   The protein of interest is subjected to proteolytic digestion and resulting peptide masses are analyzed by mass spectrometry. The sequenced peptides are searched against a protein sequence database. The service can enable identification of an unknown protein or confirmation of recombinant expressed and purified protein.

3. Whole proteome profiling (‘Shotgun’ proteomics)
   The whole proteome(s) is extracted, proteins are digested and resulting peptides fractionated, further analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Peptide identifications are based on searching against a proteome datab​ase (as available in Uniprot).

4. Quantitative Proteomics (Label-Free)
   The relative abundance of selectively expressed proteins (e.g. control vs. experimental) quantified by label-free approach (LFQ).

Bruker timsTOF Pro and NanoElute Liquid Chromatography system

Agilent Technologies 6550 iFunnel QTOF LC/MS

Incorporating breakthrough Agilent iFunnel technology, the Agilent 6550 iFunnel Q-TOF LC/MS system delivers the lowest detection levels of any high-resolution LC/MS instrument

• Agilent Jet Stream thermal gradient focusing—A precisely micro-machined sprayer surrounds ESI droplets with a sheath of superheated gas to desolvate and concentrate ions near the MS inlet for more effective sampling.
• Hexabore sampling capillary—Six independent, parallel bores enable a much larger fraction of the ions formed in the ESI spray plume to enter the mass spectrometer while reducing turbulence to maintain a stable signal.
• Dual-stage ion funnel—Novel design facilitates increased ion transfer to Q1 while evacuating the higher gas load.

Collaboration:

Please contact the responsible personnel of the core facility to set up prospective collaborations to utilize the technology available within the core facility.

Policies:

• Samples are to be submitted to the Core Facility through a dedicated inventory system.
• Samples will not be prepped and run until the user has agreed for it while submission.
• The unprepped samples will be stored in the facility not more than 2 weeks.
• The MS instruments are routinely calibrated and quality control samples are run to ensure that the machine is performing well and in case of any lack of results, they are not due to instrument problems.

*Other possible reasons for getting limited results could include:

• Lack of sufficient starting material to be detected by mass spectrometer can lead to failure in identifying protein(s).
• All proteins may not digest properly with the proteolytic enzyme ‘trypsin’ to yield the peptides that ionize well to be easily detected by the mass spectrometry.
• During in-gel digestion, some proteins cannot be easily recovered from the gel, thereby limiting the peptide availability in the sample subjected to the MS analysis.
• Samples can get contaminated before they are submitted to the core and that could hinder the sample prep procedures eventually affecting the MS run.

NOTE:​ Cancellation of service will NOT be accepted once the analysis has been started. In case desired results cannot be obtained due to the nature of the sample, interfering buffer components or low amount/ concentration of the sample, this will be informed to the collaborator soon after the MS run. Submission of service request to the core confirms acceptance of the above-mentioned policies.

Team and contact details:

Ms. Lubna Therachiyil, MSc (Interim Head, Proteomics Core)

+974 44390968
ltherachiyil@hamad.qa​
Proteomics Core facility, Hamad Medical City, Building 320, Suite 4, Translational Research Institute, Doha

Select Publications:

Therachiyil L et al. Proteomic insight towards key modulating proteins regulated by the aryl hydrocarbon receptor involved in ovarian Cancer carcinogenesis and Chemoresistance. J Proteomics. 2024 Feb 3:105108. doi: 10.1016/j.jprot.2024.105108

Krishnankutty, R. et al. An Overview of Proteomics Techniques and its Application as a Tool in Biomarker and Drug Discovery. J. Proteomics Enzymol.6, 1–13 (2017). doi:10.4172/2470-1289.1000129

Liberski, A. R. et al. Adaptation of a Commonly Used, Chemically Defined Medium for Human Embryonic Stem Cells to Stable Isotope Labeling with Amino Acids in Cell Culture. J. Proteome Res.12, 3233–3245 (2013). doi:10.1021/pr400099j

Collaborating Institutes:

Dermatology, Dept. of Urology, NCCCR, Rumailah Hospital Geriatrics/Ageing Institute, Qatar University, WWRC​​