In pursuit of utilizing combinatorial peptide libraries on beads, rapid and robust screening is one of the key steps for the success of high-throughput process. We have introduced improved structural features that greatly facilitate a MALDI-MS/MS-based sequencing, associated with easy and fast synthesis and analysis of such libraries. Whilst commonly used MS-based analysis involves in sophisticated procedures such as ladder synthesis, encoding tags are not required in our MS/MS-based sequencing platform. Fragment peaks in an acquired MS/MS should be outstanding in line with correct identification of parent mass in the preceding MS. To meet these requirements a one-bead-one-compound (OBOC) peptide library was designed by placing a positively charged arginine at C-terminus. As well as enhancing the overall ionization efficiency, arginine appended in all y-ion fragments generates a series of doublet peaks under MS/MS environments, which can speed up the sequencing process in conjunction with high accuracy. It is another strong benefit that the designed library significantly suppresses the adverse formation of sodium ion adducts, which seriously jeopardizes the sequencing, especially of peptides containing negatively charged amino acids. A peptide library constructed with D-amino acids was applied to screening against a clinically significant biomarker, C-reactive protein (CRP). Through the screening of focused libraries narrowed down from a comprehensive library, several hexamer peptide ligands were successfully identified and their binding affinity and specificity towards CRP were validated by surface plasmon resonance (SPR) and dot blot experiments.