Proteomics Services Core

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Guidelines for Submitting Samples

Always consult with the Proteomics Core manager prior to submitting (submission form) your samples for analysis. This will ensure that we understand your specific needs before submission of samples.

  • Sample types: We accept plasma or tissue samples for analysis. Please consult with us for submission of other sample types.
  • Investigators should ensure that samples are free of precipitates or large particles as this may clog or dirty the machine.
  • Be aware that certain buffers for homogenization are not compatible with the mass spec. Detergents that can be detrimental to system include the following:
    • Incompatible detergents
      • Nonidet P-40 (which can no longer be purchased; Sigma is substituting CA- Igepal 630)DSC_0409.JPG
      • Triton X-100 (or any derivative)
      • Igepal/PEG (any derivative)
      • Brij-35 (or any derivative)
      • Tween-20 OTG
      • CHAPSO
      • Type NP40/NP40 alternative
    • Incompatible buffers
      • HEPES, PBS, MES, MOPS, and Tris
        Some detergents can be separated from the sample by standard SDS-PAGE or TCA - cold acetone precipitation. However, Triton-X and Tween-20 cannot be used under any circumstances. These cannot be removed from your sample using dilution, washing, detergent spin columns, or SDS-PAGE.
    • Mass spec-friendly detergents
      • 0.05%-1% SDS
      • 0.05%-0.5% CHAPS (although not recommended)
      • N-octyl-β-glucopyranoside
      • PPS Silent Surfactant (acid-cleavable detergent)
      • Protea biosciences (anionic, zwitterionic,
        or cationic acid labile detergents)
      • Big CHAP deoxy (merck)
      • ASB series (EMD chemicals)
      • Sodium deoxycholate
    • Mass spec-friendly buffers
      • Ammonium acetate
      • Ammonium bicarbonate
      • Ammonium formate
    • Sample lysis buffers
      • Reagent 4 (Sigma C0356)
      • 8M urea with 1M ammonium bicarbonate
  • We will analyze samples in bulk to cut costs. Thus, we can advise you when your samples will be assay.
  • By checking with us first, we can also ensure that the needed calibrators, controls and reagents are on hand.

Sample preparation

  • Complete the sample submission form specific for proteomic analysis.
  • A minimum of 600ug of tissue or 15ul of plasma is required for analysis. A Bradford assay will be performed on submitted tissue samples and any samples with low protein will not be processed.
  • For power analysis, it is recommended that 6 samples per group be ran and all samples of a study must be ran together.
  • Submit only the amount requested for your assays in a microcentrifuge tube (1.5ml of 0.5ml Eppendorf tube). The core does not have the capability to spin down samples provided in non-conventional tubes (screw-cap, plates, etc.). Stock samples with large volumes or samples provided in non-conventional tubes will be returned to the core user for proper aliquoting before the assay can be performed.
  • Each sheet should be species specific. Do not mix rat and mouse samples on the same sheet.