A major unmet need in LC-MS/MS-based proteomics analyses is a set of tools for quantitative assessment of system performance and evaluation of technical variability. Here we describe 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS, and peptide identification. Applied to data sets from replicate LC-MS/MS analyses, these metrics displayed consistent, reasonable responses to controlled perturbations. The metrics typically displayed variations less than 10% and thus can reveal even subtle differences in performance of system components. Analyses of data from interlaboratory studies conducted under a common standard operating procedure identified outlier data and provided clues to specific causes. Moreover, interlaboratory variation reflected by the metrics indicates which system components vary the most between laboratories. Application of these metrics enables rational, quantitative quality assessment for proteomics and other LC-MS/MS analytical applications.

Optimal performance of LC-MS/MS platforms is critical to generating high quality proteomics data. Although individual laboratories have developed quality control samples, there is no widely available performance standard of biological complexity (and associated reference data sets) for benchmarking of platform performance for analysis of complex biological proteomes across different laboratories in the community. Individual preparations of the yeast Saccharomyces cerevisiae proteome have been used extensively by laboratories in the proteomics community to characterize LC-MS platform performance. The yeast proteome is uniquely attractive as a performance standard because it is the most extensively characterized complex biological proteome and the only one associated with several large scale studies estimating the abundance of all detectable proteins. In this study, we describe a standard operating protocol for large scale production of the yeast performance standard and offer aliquots to the community through the National Institute of Standards and Technology where the yeast proteome is under development as a certified reference material to meet the long term needs of the community. Using a series of metrics that characterize LC-MS performance, we provide a reference data set demonstrating typical performance of commonly used ion trap instrument platforms in expert laboratories; the results provide a basis for laboratories to benchmark their own performance, to improve upon current methods, and to evaluate new technologies. Additionally, we demonstrate how the yeast reference, spiked with human proteins, can be used to benchmark the power of proteomics platforms for detection of differentially expressed proteins at different levels of concentration in a complex matrix, thereby providing a metric to evaluate and minimize preanalytical and analytical variation in comparative proteomics experiments.

The characteristics of baseline drift are discussed from the perspective of error covariance. From this standpoint, the operation of derivative filters as preprocessing tools for multivariate calibration is explored. It is shown that convolution of derivative filter coefficients with the error covariance matrices for the data tend to reduce the contributions of correlated error, thereby reducing the presence of drift noise. This theory is corroborated by examination of experimental error covariance matrices before and after derivative preprocessing. It is proposed that maximum likelihood principal components analysis (MLPCA) is an optimal method for countering the deleterious effects of drift noise when the characteristics of that noise are known, since MLPCA uses error covariance information to perform a maximum likelihood projection of the data. In simulation and experimental studies, the performance of MLPCR and derivative-preprocessed PCR are compared to that of PCR with multivariate calibration data showing significant levels of drift. MLPCR is found to perform as well as or better than derivative PCR (with the best-suited derivative filter characteristics), provided that reasonable estimates of the drift noise characteristics are available. Recommendations are given for the use of MLPCR with poor estimates of the error covariance information.