  This paper presents an approach to the evaluation and validation of mass
spectrometry data for construction of an `early warning' diagnostic procedure.
We describe implementation of a designed experiment and place emphasis on the
consistent and correct use of validation based evaluation - which is a key
requirement to achieve unbiased assessment of the ability of mass spectrometry
data for diagnosis in this setting. Strict adherence to validation as a
scientific principle will however typically imply that the analyst must make
choices. Like all choices in statistical analysis, validation comes at a cost!
We present a detailed and extensive discussion of the issues involved and
propose that much greater emphasis and requirement for validation would enter
clinical proteomic science.
