Table 1.

Generalized scheme of proteomics study design employed in our laboratory

Study Steps	Objective
Step 1	Identify an important disease where improved diagnosis would change clinical management and make a measurable difference in outcome.
Step 2	Optimize SELDI conditions for the most relevant biological sample available using select groups of patients that either have or do not have the disease based on very strict clinical and/or laboratory criteria.
Step 3	Learn proteomic profiles and identify the best discriminative combination of biomarkers (PROTEME).
Step 4	Using customized bioinformatics algorithms transform the proteomic information of the PROTEME into a numeric variable (PROTEOMIC SCORE) which can be further manipulated using regular statistics.
Step 5	Evaluate the SCORE by blind testing in the population used for its development and measure intra and inter-rater variability.
Step 6	Evaluate prospectively the SCORE against relevant outcome measures in a population different than that used for its development.
Step 7	Identify component biomarkers using various proteomics methods.
Step 8	Extend pathophysiological understanding of the disease using hypothesis driven approaches stemmed from knowledge of identity of biomarkers or protein precursors.