Sample preparation protocol for bottom-up proteomic analysis of the secretome of the islets of Langerhans.

We evaluate a set of protocols for preparation of the secretome from murine islets of Langerhans for bottom-up proteomic analysis. Of the protocols evaluated, a filter-aided sample preparation based approach using sodium dodecyl sulfate as a detergent to solubilize proteins generated the most protein identifications. A total of 362 protein groups (average of 3.7 peptides/protein) were identified from the secretome using the SDS-FASP protocol; a combination of data from three protocols generated 413 protein group identifications. As expected, the identified proteins included insulin 1 and 2, somatostatin, and glucagon, the four main secreted components from islets. STRING network analysis classified the other proteins as being associated with extracellular exosomes, membrane-bounded vesicles, vesicles, and the extracellular region.