Reproducibility of a fractionation procedure for fish muscle proteomics

One of the challenges of comparative proteomics is the ability to separate and quantify all the components of highly complex mixtures of proteins, despite the fact that the concentration of their components can span several orders of magnitude. Subcellular fractionation procedures for muscle tissue have been used for some time in both gel and MS-based proteomics to address this situation, simplifying analysis by reducing the number of proteins in a given extract and improving the dynamic range by allowing larger loads per protein. Additionally, interpreting the observed changes in protein abundance may be eased by isolating a subpopulation of the whole tissue proteome. Specifi c examples of the use of these techniques for proteomic analysis include organelle and nucleus isolation, enrichment of extracts for secretory or membranar proteins, and albumin/immunoglobulin depletion of serum samples. On the other hand, since its use implies a greater number of sample processing steps than doing the whole extract, it is expected that some noise may be introduced by a fractionation procedure. Therefore, it seems important for comparative proteomic experiments to simultaneously ensure that no interbatch bias is introduced and that intrabatch noise is minimized, so that the benefits of performing this step outweigh its disadvantages.