Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is a promising tool for large-scale screening of body fluids for the early detection of human diseases. Proteins, peptides, and metabolites present in cells, tissues, or in body fluids constitute the molecular signatures of individuals. The design and generation of material-based platforms for capturing molecular signatures from body fluids has gained increasing interest in recent years. Highly selective materials are attractive candidates for a wide range of applications in biofluid proteomics. We have therefore developed a procedure based on mesoporous silica particles for the selective binding and enrichment of low molecular weight plasma/serum proteins by MALDI MS analysis ( Terracciano, R., Gaspari, M., Testa, F., Pasqua, L., Cuda G., Tagliaferri, P., Cheng, M. C., Nijdam, A. J., Petricoin, E. F., Liotta, L. A., Ferrari, M., and Venuta, S. ( 2006 ) Selective binding and enrichment for low-molecular weight biomarker molecules in human plasma after exposure to nanoporous silica particles . Proteomics 6, 3243-3250 ). Mesoporous silica beads (MSB) are able to harvest peptides from plasma and serum by means of nanosized porous channels with high surface area, while excluding large size proteins. Moreover, the absorption properties can be modified since the pore walls can be functionalized with different chemical species due to the high concentration of silanol groups at the surface. In this study, we performed derivatization of MSB with different functionalities, and we evaluated the derivatized materials for plasma and urine peptidomic profiling. Aminopropyl, N-(2-aminoethyl)-3-aminopropyl, and N,N,N' tris-carboxymethyl ethylene diamine, have been introduced onto the mesoporous silica surfaces in order to modulate selective peptide enrichment. We also explored various experimental conditions in order to optimize the performance of chemically modified MSB in the peptide profiling of human plasma and urine. These new derivatized mesoporous surfaces, in addition to the previous nonderivatized MSB, constitute an extended and reliable platform of five distinct chromatographic phases with defined surface functionality and porosity. Several plasma and urine peptides were extracted from derivatized MSB and then profiled by MALDI-TOF MS. The reproducibility of sample preparation by different functionalized beads was evaluated via three replicate analyses of plasma and urine samples. Lower coefficients of variation in the mass values and peak intensities resulted for plasma in comparison to those of urine samples; nevertheless, these where satisfactory for diagnostic purposes. For human urine, a linear correlation was found between spiked peptide concentrations and their peak areas (R(2) > 0.98) with a limit of detection in the low-nanogram per milliliter range, thus confirming the high sensitivity of the methodology, previously demonstrated for human plasma. Different panels of peptide repertoires have thus been collected from highly porous substrates chemically conjugated with different functional groups, and these may be used in biomarker discovery for disease diagnosis.