Challenges Facing Complete Human Proteome Analysis

Abstract

Mass spectrometry (MS) is the most widely used technology for proteome analysis, and MS-based proteomics platforms have identified over 10,000 human proteins in single-state cellular targets. Here, we review recent advances towards complete analysis of the human proteome. The main obstacles are the enormously wide dynamic range and huge complexity of the proteome. New technologies of sample preparation, protein/peptide separation and MS acquisition have been developed to tackle these issues. Pre-fractionation approaches, such as multidimensional separations prior to LC-MS/MS, have been introduced, but the total measurement time increases as the fraction number increases. Alternative approaches using high-resolution LC without pre-fractionation have also been developed, because high sample recovery is expected if the number of sample pretreatment steps is minimized. Although technical and methodological issues remain, human proteome analysis covering 7,000 - 10,000 proteins is currently feasible.