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Harvesting Protocol for Stool

This protocol explains how to harvest stool for metabolomics and lipidomics assessments by Gigantest.

Table of Contents

Starting Sample Quantity

For targeted, untargeted lipidomics, metabolomics (endogenous metabolites), drug & chemical detection:

  • Sample weight: 20 mg < sample weight < 100 mg

The bigger the sample quantity, the better the chance of detecting metabolites with lower intensities. We recommend n=3-5 (at least) for preliminary data, n > 5 for publication. If you cannot have the recommended sample quantity, please let us know so we can find the best solution.

The following protocol is for ONE sample. To collect multiple samples, use multiple tubes for each step.

Harvesting the Stool Sample

  1. Make sure you have the following materials before you start harvesting:
    • Liquid nitrogen to snap freeze samples
  2. Place the stool sample into a tared 2 mL tube and record the stool sample weights. It’s essential to record the stool weights to allow for the normalization of metabolite intensity for comparison purposes.
  3. Snap freeze the 2 mL tube containing the stool sample and store at -80˚C in a sample box.
  4. Send sample weights to

Packaging & Shipping

  • Place the sample boxes containing your samples in a Styrofoam box full of dry ice making sure to surround the sample boxes on all sides.
  • Email the Sample Information Form to
  • Ship via FedEx Priority Overnight or FedEx Standard Overnight, or other express carriers of your choice. Please include our phone number, (667) 312-2914, on the shipping label so that the carrier can contact us when they arrive at our location. Please also select the “Direct Signature Required” option under the “Signature options”.

Ship to:


31 Light Street

3rd Floor

Baltimore, MD 21202

If your samples are located in Maryland, please email Gigantest at or call (667) 312-2924 to arrange a sample pick-up. Make sure to keep the samples on dry ice.