Protein chip datamanager 3

Second-voided urine samples were collected from each patient and, for ccRCC patients, before nephrectomy. The samples were processed as previously reported [20 ] and stored at -80°C until use. Prior to each analysis, the instrument performance was checked by the ProteinChip OQ kit (BIORAD). All the samples were analysed within a short time frame when the machine was working to standard. The SELDI analysis was carried out by loading 10 μg proteins from each patient in duplicate on CM10 ProteinChip array (BIORAD, cat. C57-30075) and following our previously described protocol [23 (link)]. After acquisition, the spectra were analysed by Protein chip DataManager™ 3.5 software (BIORAD, Hercules, CA, USA). The analysis was performed in a m/z range from 3,000 to 30,000 daltons, considering as real peaks those with S/N and a valley depth ratio greater than 4. All the spectra were normalized by means of total ion current. The reproducibility of the SELDI analysis, assessed as previously described [20 ], was comparable to that in our previous works [22 (link), 23 (link)]. Only mass peaks showing a statistically significant different expression (p<0.05) between cases and controls were considered for further analyses.