Novel approaches for the qualitative and quantitative proteomic analysis by nanoscale LC-MS ap-plied to the study of protein expression response in depleted and undepleted serum of Gaucher patients under going enzyme replacement therapy are presented. Particular emphasis is given to the method reproducibility of these LC-MS experiments without the use of isotopic labels. The level of chitotriosidase – an established Gaucher biomarker – was assessed by means of an abso-lute concentration determination technique for alternate scanning LC-MS generated data. Disease associated proteins – including fibrinogens, complement cascade proteins, and members of the high-density lipoprotein serum content – were recognized by various clustering methods and sorting and intensity profile grouping of identified peptides. Condition unique LC-MS protein sig-natures could be generated utilizing the measured serum protein concentrations and are pre-sented for all investigated conditions. The clustering results of the study have also been used as input for gene ontology searches to determine the correlation between the molecular functions of the identified peptides and proteins.