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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 typicallyarXiv:math/0510188v1 fatcat:wjapty5dpnbc3jllkyhanzip7q