Dec 04, 2025
Tissue Sample Preparation for Biochemical Analysis
- Yue Ma1
- 1Van Andel Institute
Protocol Citation: Yue Ma 2025. Tissue Sample Preparation for Biochemical Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2ly43kwlx9/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: July 21, 2025
Last Modified: December 09, 2025
Protocol Integer ID: 222847
Keywords: ASAPCRN, tissue samples for general metabolomics profiling, general metabolomics profiling, tissue sample preparation for biochemical analysis, biochemical analysis, tissue sample preparation, tissue sample
Funders Acknowledgements:
ASAP
Grant ID: ASAP-000592
Abstract
To prepare tissue samples for general metabolomics profiling by GC-MS or LC-MS.
Guidelines
5. Add one sample to the mortar and grind to a homogenized powder with the pestle
6. Use the cooled spatula to transfer to the labeled screw cap tube
7. Return tube to LN2 while processing other samples.
8. Wipe mortar, pestle and spatula with paper towel or a Kim Wipe prior to processing the next sample. “Rinsing” tools in LN2 can also help remove residual sample.
9. Store tissues at -80°C if not immediately weighing.
Materials
Tissue Collection:
1. Pre-labeled foil squares (3”)
2. Dissection tools
3. Isoflurane vaporizer
4. Liquid nitrogen
5. Aluminum block and tongs
Tissue Pulverization and Weighing:
1. Liquid nitrogen
2. Dry ice
3. Mortar and pestle
4. Spatula
5. Tweezers
6. Ceramic bead ruptor tubes
7. Screw cap tubes
Troubleshooting
Collection Protocol
Fill a cold safe container with liquid nitrogen (LN2) and submerge the flat plates (grip) of the aluminum tongs. Be careful not to allow the tong handles to be submerged. It may be necessary to have extra LN2 on hand to refill the container as it evaporates. If an aluminum block will be used for sample processing, place this on wet ice to cool.
Sedate the animal using isoflurane vaporizer.
Collect tissues by carefully removing, immediately folding into the pre-labeled foil square, smashing between the cold aluminum tongs, and dropping into LN2. Once samples are snap frozen, they should always be kept at -80°C. (If the tissue collection tongs are not available, drop sample folded into foil square directly into LN2.)
Pulverization Protocol
Label a set of screw cap tubes (5ml tubes are usually needed for full liver collection from mice; for smaller tissue samples, 2ml tubes are usually sufficient)
Float samples (still wrapped in foil) in LN2 during pulverization process. Fill a second LN2 safe container with LN2
Cool mortar, pestle, and spatula on dry ice prior to starting pulverization and perform pulverization on dry ice
Briefly dip the mortar and pestle into the other container of LN2 to further cool them prior to pulverizing each sample. Leaving some LN2 to evaporate from the mortar during pulverization will help keep tissue cold. Pulverized tissue thaws immediately when warmed; if the sample seems to be “sticky” this means it is beginning to thaw.
Add one sample to the mortar and grind to a homogenized powder with the pestle
Use the cooled spatula to transfer to the labeled screw cap tube
Return tube to LN2 while processing other samples.
Wipe mortar, pestle and spatula with paper towel or a Kim Wipe prior to processing the next sample. “Rinsing” tools in LN2 can also help remove residual sample.
Store tissues at -80°C if not immediately weighing.