The disclosure relates to an in vitro technology of detecting presence of a plaque particle, isolating the plaque particle followed by its composition analysis in several diseases states or before the disease sets in. A mechanism and a process leading to plaque formation, identifying a component in the mechanism of plaque formation, an identification of a biomarker for diagnosis/early diagnosis of plaque associated disease is described. A method of screening a candidate agent as an anti-plaque agent using flow cytometer, mass spectrometer and specific biomarkers is performed. Provided also are kits for use in practicing embodiment of the methods. A plaqueproteome database is also generated with novel protein sequences for diagnosis and specific antibodies for specific proteins are also disclosed.