Subject area	Biology
More specific subject area	Rat and human pancreatic beta cell proteomics
Type of data	Excel tables
How data was acquired	Label-free alternate-scanning LC-MS proteomics; Nanoscale LC separation of tryptic peptides was performed with
	a nanoACQUITY system (Waters Corporation), equipped with a
	Symmetry C18 5 mm, 2 cm 6180 mm precolumn and an Atlantis
	C18 3 mm, 25 cm 675 mm or a Atlantis C18 3 mm, 15 cm
	675 mm analytical reversed phase column (Waters Corporation).
Data format	Raw/Analyzed
Experimental factors	Proteomes of rat alpha and beta cells were studied immediately after cell isolation, without in vitro culture or treatment. Proteins were typically extracted within 4 h of animal killing. Human beta cells were prepared from islet-enriched pancreas fractions, cultured for 6–14 days after human organ procurement. Selected fractions cleared for research were then trypsin-dissociated into single cell suspensions and FACS-sorted according to cell size, granularity and zinc content to an average insulin-purity of 60%. Proteomes of these cells was studied immediately after cell isolation without additional treatment or further culture.
Experimental features	Proteomes were recorded using label-free LC-MS/MS. Accurate mass precursor and fragment ion LC-MS data were collected in data independent, alternate scanning (LC-MSE) mode of acquisition [2,3]. Biological interpretation of the “relative molar amount units” was done after geometric normalization to a network of stable reference proteins [4–8]
Data source location	Rat data: Waters Corp., Manchester, UK, Analyst: J.P.C. Vissers
	Human data: Department of Medical Biochemistry, Academisch Medisch Centrum, Amsterdam, the Netherlands, Analyst: G. Kramer
Data accessibility	Raw data uploaded to ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers
	PXD001539: human data
	Project DOI: 10.6019/PXD001539
	Reviewer account details:
	Username: reviewer99564@ebi.ac.uk
	Password: pJzPiCIj
	PXD001816: rat data
	Project DOI: 10.6019/PXD001816
	Username: reviewer43213@ebi.ac.uk
	Password: y2B5bYLW