Table 1.

Recommended practices for clinical applications of protein profiling by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

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 limits of detection 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 10 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