The subject of this study was to evaluate the impact of dynamic exclusion and protein size on the capability of database search programs to identify protein in tandem mass spectrometry (MS/MS) experiments. Through the two stages of mass fragmentation, MS/MS spectrometry allows for an identification of peptides. Furthermore, the identification of proteins is heightened with the use of dynamic exclusion and fractionation. This bioinformatics study was applied to mass spectra from the brain macrophages of healthy wild type mice and mice exposed to an infection. The database search software PEAKS was used to identify peptides and proteins across protein sizes (fractionations) and exclusion options. Parameter specifications to optimize the identification of proteins and peptides were: parent mass error tolerance (15.0 Da) and fragment mass error tolerance (0.1 Da) specifications. After analysis, proteins such as Beta-globin (A8DUK40) and Actin cytoplasmic 1 (ACTB) were identified.