Endogenous S-nitrosoproteome in colorectal cancer patients

Total lysate of tumorous and adjacent normal tissues from each colorectal cancer patient are followed by S-alkylating biotin switch strategy. All biotinylated peptides are analyzed by label-free quantitation and LC-MS/MS analysis. All peak lists from 66 raw MS/MS spectra were processed to mgf format by Mascot Distiller v2.1.1.0. The datasets were batch-searched and combined searched by Mascor v2.2 against the Swissprot v 57.8 human database. PEO-iodoacetyl-biotin (C, +414 Da), Caebamidomethyl (C) and oxidation (M) were specified as variable modifications. Peptides were considered to be identified if the Mascot individual ion score was higher than the Mascot identity score (p less than 0.05). To evaluate the false discovery rate in protein identification, a decoy database search against a randomized decoy database created by Mascot using identical search parameters and validation criteria were also performed. The search results in Mascot were exported in eXtensive Markup Language (XML) data format.