Low-abundance protein detection in biological samples is one of the main challenges in proteomics investigations. One approach that makes the detection of rare species possible is the treatment of biological samples with solidphase combinatorial peptide ligand libraries. However, the use of combinations of ligands opens an uncertainty in that, since the diversity of the library is very large, aliquots of beads sampled from the library might not have fully comparable bead species each time. Reproducibility of experimental data with highly diverse libraries is therefore a main concern to address. This paper reports reproducibility data when aliquots of similar and different volumes of libraries are used at a certain sample to library ratio. Eluates from ligand libraries and other fractions are analyzed using various complementary methods such as two-dimensional gel electrophoresis, immunoassay and mass spectrometry. The collected data show a high level of consistency from sample to sample when processed with similar and variable bead volumes. Analytical determinations are all convergent with each other in considering the similarity of results. It is anticipated that this demonstration reinforces the possibility that differential proteomics studies, in particular for the discovery of protein targets of interest, can effectively be accomplished with combinatorial peptide libraries.