Challenges of sample preparation
Taking a sample from its natural environment has drastic effects even within a very short timeframe. The sample tries to adapt to its new situation and the cellular activity continues causing the release of enzymes. This leads to both degradation and alteration of the levels and composition of proteins, peptides and post-translational modifications. Therefore, downstream analytical results reflect a mixture of the in vivo proteome and ex vivo degradation products.
Continuously throughout the sample preparation process, different freeze/thaw steps and homogenization assist enzymatic activity by providing access to substrates not normally encountered by enzymes, thereby facilitating and accelerating degradation. Vital information about your sample may be distorted or even completely destroyed.
The importance of correct sample preparation cannot be overstated for supporting reproducible proteomics results. Sample quality is crucial and must be considered throughout the whole experiment. In this section, you will find helpful information about how to ensure that the sample quality of your samples is maintained through-out your work flow.
Figure 3: Overview of the rapid effect of post-mortem degradation and changes throughout sample preparation
[image courtesy of Denator, Sweden]
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