Data for: Urinary peptidome analyses for diagnosis of chronic kidney disease in dogs
CE-MS analyses were performed using a Beckman Coulter Proteome Lab PA800 capillary electrophoresis system (Beckman Coulter, Fullerton, USA) on-line coupled to a micrOTOF II MS (Bruker Daltonic, Bremen, Germany). The electro-ionization sprayer (Agilent Technologies, Palo Alto, CA, USA) was grounded, and the ion spray interface potential was set to –4.5 kV. Data acquisition and MS acquisition methods were automatically controlled by the CE via contact-close-relays. Spectra were accumulated every 3 s, over a range of m/z 350 to 3000. In the next step the MosaiquesVisu software package was applied to deconvolute mass spectral ion peaks, because ionization produced ions at different charged states from the original urinary peptides. This deconvolution step groups these differently charged ions into single peptides with unique real mass. Only signals observed in a minimum of three consecutive spectra with a signal-to-noise ratio of at least 4 were considered. Signals with a calculated charge of 1+ were automatically excluded to minimize interference with matrix compounds or drugs. Capillary electrophoresis migration time and MS-detected mass were normalized by the definition of 950 clusters of peptides covering a range of 17.23 to 47.74 minutes in CE migration time and 807 to 16399 kDa in molecular mass. Samples were normalized by peptide abundance (intensity) calibration based on 141 endogenous internal urinary polypeptide standards displaying the highest frequency and stability in all analysed samples, to compensate for differences in hydration status and urine volume between dogs. Each polypeptide present in the list was defined by its normalized migration time [min], molecular mass [kDa], and signal intensity detected. Using a Microsoft Structured Query Language database, all detected polypeptides were deposited, matched, and annotated in order to allow for further comparison between groups. The criteria applied to consider a polypeptide identical was that within different samples, the mass deviation was lower than 50 ppm for masses < 4 kDa, 150 ppm for masses >6 kDa, and between 50-150 ppm for masses between 4 and 6 kDa. Acceptable migration time deviation was between 1 and 2.5 minutes.