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  • 1.  setting up a proteomics core lab

    Posted 02-15-2023 09:09

    I was wondering whether there is information at ABRF on how to setup a new state of the art proteomics laboratory. Personnel, equipment, space, lab specifics, etc.; anything that is required for starting from scratch.

    Thanks much!

    Chris 



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    Chris Turck
    Prof.
    Max Planck Institute of Psychiatry
    Munich TX
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  • 2.  RE: setting up a proteomics core lab

    Posted 02-16-2023 09:54
    Hi Chris,

    There was a very nice presentation on this at the 2022 MAD SSCi meeting (https://madssci.abrf.org/resources/).  I'm not sure if it covers everything you are interested in, but the video is available on our YouTube channel (https://www.youtube.com/watch?v=hqTjxsjHyYA).  I would be happy to connect you to the presenter if you think it would be useful.

    Roxann







    Original Message


  • 3.  RE: setting up a proteomics core lab

    Posted 02-16-2023 10:21

    Hi Chris,

    I work at the IDeA National Resource for Quantitative Proteomics located at UAMS in Little Rock Arkansas as a staff scientist.  We don't have a step by step guide for starting up a proteomics laboratory but we are currently running one and would be willing to share what we are doing.  

    Let me know if you want to set up a video conference with our core directors.

    Dennis Province



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    Dennis Province
    Principal Staff Scientist
    University of Arkansas for Medical Sciences
    Little Rock AR
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    Original Message


  • 4.  RE: setting up a proteomics core lab

    Posted 02-16-2023 13:33

    Chris,

    This depends a lot on your budget, user base, sample load and application range. So I don't believe there can be a general guidance. I'll dot down what I have.

    I have been running a single-person proteomics core serving a relatively small user base since 2008 (two different institutes). If I'm to build another core like this, access to a state-of-art mass spectrometer (for now, Bruker TIMS TOF or Thermo Ascend) and budget to upgrade every 5-7 years plus service contract is a must. Equally important is  a good computer workstation and some commercial software licenses to handle proteomics data.

    On personal side,  you need to look at talent you have and again the projects you are looking at. Proteomics is 3 parts: sample prep, LC-MS/MS, and data processing/informatics. Most trainees I work with can handle sample prep with some initial guidance, so I won't invest in that, but would consider having equipment for users to do digestion in the proteomics lab. I'm fairly good on the instruments and love any project that need additional tinkling (beyond canned methods), but having someone that can choose a canned method and talk to tech support as needed is probably good enough. On data processing side, you need to define where a proteomics project ends. Who's going to dig into the large dataset and come up with a story? I find a lot of data I delivered underused, but at the same time, don't believe it's my job as a core director.

    Space wise, a mass spec is better off in a separate room to keep the noise to itself. It usually needs separate AC, exhaust, power (especially in US), and nitrogen supply (usually compressed air and nitrogen generator). 

    This will be the minimum, from here, sky is the limit... My two cents.

    Yan



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    Yan Wang
    Director, Mass Spectrometry Facility
    NIH/NIDCR
    Bethesda MD
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    Original Message


  • 5.  RE: setting up a proteomics core lab

    Posted 02-16-2023 15:07

    Dear Chris:

    I can help. I am the Core Director (Technical) of the Emory University Proteomics Core. Please email me at pbagchi@emory.edu.

    Best wishes,

    Pritha



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    Pritha Bagchi
    Emory University School of Medicine
    Atlanta GA
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    Original Message


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