It doesn't matter if different protocols should be performed for the two organs. All the proteins are in the interest, as a quantitative proteomics experiment will be performed on them.
Use chloroform:methanol (2:1, -20 oC) to homogenize your sample (5:1 ratio over sample volume). After centrifugation, you will find 2 separate layers. There should be a layer of interphase pellet (protein). Wash the pellet with ice-cold methanol, vortex, and then centrifuge at 12000 rpm, 4 oC for 10 mins. Remove the methanol and then allow the sample to completely dry. Re-suspend the dried pellet with appropriate buffer and then you can do the proteomics from there.
J Vis Exp. 2014; (88): 50374. Published online 2014 Jun 25. doi: [10.3791/50374] PMCID: PMC4205887 NIHMSID: NIHMS710106 PMID: 24998772 A Method for Mouse Pancreatic Islet Isolation and Intracellular cAMP Determination