Well-plate uFASP for proteomic analysis of single pancreatic islets

ABSTRACT: Filter-aided sample preparation (FASP) is widely used in bottom-up proteomics for tryptic digestion. However, the sample recovery yield of this method is limited by the amount of starting material. While ~100 ng of digested protein sample is sufficient for thorough protein identification, proteomic information gets lost after digestion of samples with a protein content < 10 µg due to incomplete peptide recovery from the filter. By reducing the filter area as well as the volumes of all reagents, we developed and optimized a well-plate µFASP device and protocol that is suitable for ~1 µg protein sample. In 1 µg of HeLa digest, we identified 1295 ± 10 proteins with our method followed by analysis with liquid chromatography–mass spectrometry. In contrast, only 524 ± 5 proteins were identified with the standard FASP protocol while 1395 ± 4 proteins were identified in 20 µg after standard FASP as a benchmark. Furthermore, we used our method to conduct a combined peptidomic and proteo-mic study of single islets of Langerhans. Here, we separated neuropeptides from single islets as effluents from a ⌀ 1 mm molecular cut-off filter and digested the remaining on-filter proteins for bottom-up proteomic analysis. Our results indicate inter-islet heterogeneity for expression of proteins involved in glucose catabolism, pancreatic hormone processing and secreted peptide hormones. We consider our method to provide a useful tool for proteomic characterization of samples where biological material is scarce.

INSTRUMENT(S): Synapt MS

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Pancreatic Islet, Hela Cell

SUBMITTER: Erik Jansson  

LAB HEAD: Erik Jansson

PROVIDER: PXD029039 | Pride | 2022-04-01

REPOSITORIES: pride