Mass spectrometry-based urine peptidomics analyses suffer from two major sources of variance [18] : analytical issues including mass spectrometric ion suppression; and biological issues including dilution of urine by different hydration states of the urine donors. To standardize amount of urine peptides for comparative analysis, we have quantified each extracted urine peptidome by the TNBS assay [28] and 3 nmol of peptides were subjected to the downstream LC-MALDI-TOF profiling analysis. The initial step in our biomarker discovery effort was to collect urine peptide spectra by LC-MALDI-TOF profiling from the 56 urine samples. The MS spectrum of each HPLC fraction was analyzed by "MASS-Conductor" software (Ling, unpublished) , which extracts peaks from raw MALDI spectra, enables common peak alignment, generates consensus representative peaks across all spectra via two-dimensional hierarchical clustering of both mass/ charge and the HPLC fractions, and normalizes peak signal measurements.