IP-Works » Protein pulldown analysis services

Protein pulldown analysis services

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Overview

  • Advances in mass spectrometry have greatly improved understanding of protein complex assembly and protein–protein interactions.
  • Our IP-works service has helped thousands of researchers characterize protein complexes and identify novel protein-protein interactions.
  • This service utilizes state-of-the-art proteomics technology to provide a comprehensive characterization of your enriched samples.

Our Recommendations

For the most successful outcome to your experiment we recommend the following:

  • Samples should be prepared in biological triplicate. For a control and test pair you would submit six total tubes.$1500 is the three sample price.
  • Unsure if your pulldown is working? If you don’t want to make the investment in biological triplicates, contact us and we can help steer you towards our other services that can be used for optimization.
  • If you have not optimized your elution we recommend submitting the pulldown on the beads. For sample submission, beads should be washed, wash buffers removed, the matrix pelleted and frozen.
  • For shipping, place frozen beads in a secondary container such as a 50mL screw cap tube or small box. Samples should be shipped on dry ice for overnight delivery.
  • Complete a sample submission form and return a copy to orders@msbioworks.com
  • We recommend shipping samples for next-day delivery with FedEx or UPS. Ship Samples for delivery Tuesday – Thursday.  Our shipping address is:

    MS Bioworks
    3970 Varsity Drive
    Ann Arbor
    MI,
    48108
  • Leverage our expertise, if you have questions call and ask for our technical support. We have processed tens of thousands of pulldown samples. Use our experience to help achieve a positive outcome.

Steps involved

  • Sample preparation: Our preference is to process eluted proteins using SDS-PAGE. 50% of the elution is processed using short-gel electrophoresis. In-gel digestion with trypsin is used to produce a mass spec compatible sample in a robust, routine, reproducible manner. On-bead digestion is available on request but beware not all beads are created equal and without process optimization this can introduce avoidable noise into your data.
  • Proteomics analysis: Digested proteins are analyzed by LC-MS/MS using Data Independent Acquisition (DIA) on Thermo ScientificTM VanquishTM Neo coupled to an OrbitrapTM AstralTM.
  • Data analysis: Data are processed with DIA-NN (Aptila Bio) with further processing in The Perseus computational platform for comprehensive analysis of (prote)omics data (Nat Methods 13, 731–740 (2016))

Deliverables

  • Written Report containing details of your samples, our methods and a summary of the data.
  • An Excel workbook containing the qualitative and quantitative proteomics data

An example report is available upon request.