Computational protocol: Isolation and mass spectrometry analysis of urinary extraexosomal proteins

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[…] The MS raw files were processed with Proteome Discoverer 1.4 (Thermo Fischer, Bremen, Germany), using the Sequest algorithm, searching against reviewed human protein database generated from sequences obtained from Uniprot (May, 2015: 148764 entries). Enzyme specificity was set to trypsin. The initial parent and fragment ion maximum mass deviation was set to 20 ppm and 0.6 Da, respectively. The search included methionine oxidation as variable modification as well as N-terminal acetylation. Up to four missed cleavages were allowed and peptides had to be fully tryptic. A strict false discovery rate (FDR) was set to 0.01. […]

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