Sample size determination in clinical proteomic profiling experiments using mass spectrometry for class comparison

• Published in: Proteomics (Weinheim) 2009, Vol.9 (1), p.74-86
• Main Authors: Cairns, David A, Barrett, Jennifer H, Billingham, Lucinda J, Stanley, Anthea J, Xinarianos, George, Field, John K, Johnson, Phillip J, Selby, Peter J, Banks, Rosamonde E
• Format: Article
• Language: English
• Subjects: Analysis of Variance; Analytical, structural and metabolic biochemistry; Applied microbiology; Biological and medical sciences; Blood Proteins - analysis; False discovery rate; Fundamental and applied biological sciences. Psychology; Humans; Mass Spectrometry; Microbiology; Miscellaneous; Plasma - chemistry; Power; Protein Array Analysis - methods; Proteins; Proteome - analysis; Research Design; Sample Size; Type I error; Vaccines, antisera, therapeutical immunoglobulins and monoclonal antibodies (general aspects)
• ISSN: 1615-9853; 1615-9861
• DOI: 10.1002/pmic.200800417

Mass spectrometric profiling approaches such as MALDI-TOF and SELDI-TOF are increasingly being used in disease marker discovery, particularly in the lower molecular weight proteome. However, little consideration has been given to the issue of sample size in experimental design. The aim of this study was to develop a protocol for the use of sample size calculations in proteomic profiling studies using MS. These sample size calculations can be based on a simple linear mixed model which allows the inclusion of estimates of biological and technical variation inherent in the experiment. The use of a pilot experiment to estimate these components of variance is investigated and is shown to work well when compared with larger studies. Examination of data from a number of studies using different sample types and different chromatographic surfaces shows the need for sample- and preparation-specific sample size calculations.