Table 1.

Recommended practices for clinical applications of protein profiling by MALDI TOF MS

Preanalytical	Evaluate optimum patient preparation
	Identify optimum procedures for specimen collection and processing
	Analyze specimen stability
	Develop criteria for specimen acceptability
Analytical	Prepare calibrators for mass, resolution, and detector sensitivity
	Use internal standards
	Automate specimen preparation
	Optimize methods to yield highest possible signals for peaks of interest
	Identify sequences of peaks of interest
	Develop calibration materials for components of interest
	QC: prepare/identify at least two concentrations of control material
	Evaluate reproducibility (precision)
	Evaluate LOD and linearity
	Evaluate reference intervals
	Evaluate interferences such as hemolysis, lipemia, renal failure, acute-phase responses
	Develop materials or programs for external comparison/proficiency testing of analyzers
Postanalytical	Analyze each spectrum to identify peaks before applying diagnostic algorithms
	Develop criteria for the acceptability of each spectrum based on peak characteristics
	Use peaks rather than raw data as the basis for diagnostic analysis
	Use caution in interpretation of peaks with m/z<1200
	Select peaks with high intensities and sample stability for diagnosis
	Select approximately equal numbers of peaks that increase and decrease in intensity as diagnostic discriminators
	In developing a training set for diagnosis, careful clinical classification of patients is essential
	Clinical validity depends on having a typical rather than highly selected population of patients
	The number of training specimens should be at least ten times the number of measured values
	Any clinical application should use a fixed training set and algorithm for analysis
	Any analysis should provide a numerical value
	Diagnostic performance should be evaluated with ROC curves to select cutoffs
	A sensitivity analysis should be performed of the necessary precision for accurate diagnostic performance
	There should be QC procedures for daily verification of software performance

Adapted from Hortin [26].