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Harvesting Protocol for Suspension Cells

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

Table of Contents

Starting Sample Quantity

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

  • Cells: 2 to 10 million cells if possible
  • Media:  50 μL < sample volume < 250 μL

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 Suspension Cells

  1. Make sure you have the following materials before you start harvesting:
    • Cold phosphate buffered saline (PBS)
    • Liquid nitrogen to snap freeze samples
  2. Count and record the number of cells for each sample. It’s essential to record the cell numbers to allow for the normalization of metabolite intensity for comparison  purposes.
  3. Pour your cells and media into a 50 mL tube
  4. Centrifuge the 50 mL tube at 1500 rpm for 10 minutes at 4˚C to separate the media from the cells.

Media Sample Collection (optional)

If you want to assess metabolites in the MEDIA (in addition to assessing metabolites in the cells), follow steps 5 through 7 to collect a media sample. Otherwise, skip to step 8 to collect the cell samples.

  1. Transfer 2 mL of the media to a new 2 mL tube
  2. Label the tubes "Media - Sample Name / Code".
  3. Snap freeze the 2 mL tube containing the media sample and store at -80˚C in a sample box.

Cell Sample Collection

  1. Aspirate out all the media from the 50 mL tube (do not aspirate the cells).
  2. Add 1 mL cold PBS to the 50 mL tube to resuspend the cell pellet.
  3. Transfer PBS and cells to a new 2 mL tube
  4. Centrifuge the 2 mL tube at 1500 rpm for 10 minutes at 4˚C to separate the PBS from the cells.
  5. Aspirate out all the PBS from the 2 mL tube leaving the cell pellet in the tube.
  6. Label the tubes "Cells - Sample Name / Code".
  7. Snap freeze the 2 mL tube containing the pellet in liquid nitrogen and store at -80˚C in a sample box.

Packaging & Shipping

  • Place the sample boxes containing your samples ( cells and optionally media ) 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.