| Objective To develop and establish the new and early—warning diagnostic module for chronic allograft nephropathy using surface enhanced laser desorption / ionization-time of flight-mass spectrometry (SELDI-TOF-MS). Methods Serum peptide peaks were detected by SELDI-TOF-MS and weak cation exchange(CM10), which were from the healthy individuals, the patients with chronic kidney failure, long-term survival patients with well-functioning kidney allograft (LS) and the patients with chronic allograft nephropathy(CAN), and then biomarker candidates were screened through the analysis of database with Biomarker Wizard and Biomarker Pattern softwares. Results 85 protein spectra of interest were detected between the LT and CAN group, 6 of them (m/z 2476.0, 3078.7, 3190.5, 4076.5, 4506.0, 6178.4) statistically showed significant difference, the novel biomarker (m/z 3078.7) differentiated LT from CAN, it was upregulated in the former group and downregulated in the latter group, its sensitivity and specificity were 87.5% and 81.8% respectively. The structure of Decision Tree Classification comprised of two terminal nodes, and its complexity was 0.068, The discriminatory weight of the peptide (m/z 3078.7) was scored 100 between two groups, and the weight of others were all scored less than 100, it is a single biomarker, the relative cost in discriminating two groups is 0.307 and the gains will reach 1 with the larger patient population. Conclusions The biomarker candidates detected and characterized by SELDI-TOF-MS is beneficial to predicting and uncovering a heterogeneous disease.
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