Integrated multi-level quality control for proteomic profiling studies using mass spectrometry

Using data from a SELDI profiling study of serum from patients with different levels of renal function, we show how the algorithms described in this paper may be used to detect systematic variability within and between sample replicates, pooled samples and SELDI chips and spots. Manual inspection of those spectral data that were identified as being of poor quality confirmed the efficacy of the algorithms. Variance components analysis demonstrated the relatively small amount of technical variance attributable to day of profile generation and experimental array.Using the techniques described in this paper it is possible to reliably detect poor quality data within proteomic profiling experiments undertaken by MS. The removal of these spectra at the initial stages of the analysis substantially improves the confidence of putative biomarker identification and allows inter-experimental comparisons to be carried out with greater confidence.Clinical proteomic profiling experiments using high throughput mass spectrometry (MS) technologies such as matrix assisted laser/desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) and the derivative surface enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF-MS) have provided encouraging and exciting results over the past few years [1-4]. However, many studies have been the subject of debate, both in terms of the reproducibility of results and regarding issues of technical and experimental design [5-7]. A common criticism has been the difficulty in identifying the protein or peptide signified by the specific informative peak(s) in the mass spectrum, and indeed if it has been possible, then the identified protein has often been of relatively high abundance and not disease-specific [8].There is now an expanding literature which describes good practice in undertaking such experiments. Reanalysis of published data has raised a number of important issues relating to experimental design and dry-la