The extraction of proteins from tough tissues, such as muscle and lung, generally requires extensive mechanical disruption, or chemical or enzymatic treatment to recover and adequately analyze their proteome. Mortar and pestle grinding, pulverization in liquid nitrogen, homogenization with a Dounce, or rotor-stator homogenizers are some of the classical methods used. However, these manual methods are labor-intensive, time consuming, and prone to sample-to-sample variability and to cross-contamination. In addition, these traditional methods, while effective, can not be easily adapted for use with difficult samples. We report efficient disruption using the PBI Shredder System (The PCT Shredder or The SHREDDER SG3) for diverse applications: proteomic profiling, isolation of nucleic acids, and extraction of intact mitochondria. The sample types included elastic tissues such as lung and muscle; tough samples such as leaves; hard samples such as seeds; hard-to-disrupt organisms such as C. elegans; and arthropods. Some Shredder-disrupted samples were subjected to additional processing using pressure cycling technology (PCT) to maximize yield. Using the Shredder System, we isolated protein from rat skeletal muscle and human ovarian tumor tissue, as well as from C. elegans and dry rice grains. We also obtained good yields of DNA from apple seeds and whole ticks, as well as DNA greater than 140 kb in length from spinach leaves. Additionally, we have shown that the PBI Shredder System can be used for rapid and efficient extraction of RNA from frozen rat lung tissue. The System was also used to isolate intact and functional mitochondria from fresh skeletal muscle.