Among the emerging quantitative proteomics technologies, isobaric tags for relative and absolute quantification (iTRAQ) allows concurrent protein sequence identification and relative quantification of those peptides with known protein sequences in up to eight different biological samples in a single experiment [20] . However, due to its limited throughput and current cost, iTRAQ is not feasible for simultaneous comparison of the large number of disease subjects needed to achieve the discovery of differential features with sufficient statistical power. As an alternative, a label-free liquid chromatography-mass spectrometry (LC-MS)-based approach has been applied as a quantitative biomarker discovery method. The label-free LC-MS approach can compare and quantify peptides with precision and accuracy comparable to those based on isotope labeling [21] . Although LC/ESI mass spectrometry is typically used in label-free quantitative proteomics, matrix-assisted laser desorption/ionization-timeof-flight (MALDI-TOF) mass spectrometry is increasingly being used and demonstrates low average coefficients of variation for all peptide signals across the entire intensity range in all technical replicates [22, 23] . Using the label-free LC/MALDI-TOF profiling approach, we previously discovered candidate urine peptide biomarkers of renal transplant rejection [19, 24] . Subsequent urine peptide biomarker validation [19] by multiple reaction monitoring (MRM) [25, 26] showed significant correlation between the urine peptide measurements obtained from label-free MALDI-TOF and from MRM using stable isotope-labeled synthetic marker analogues to derive absolute quantification.