Block Design with Common Reference Samples Enables Robust Large-Scale Label-Free Quantitative Proteome Profiling.

ABSTRACT: Label-free quantitative proteomics has become an increasingly popular tool for profiling global protein abundances. However, one major limitation is the potential performance drift of the LC-MS platform over time, which, in turn, limits its utility for analyzing large-scale sample sets. To address this, we introduce an experimental and data analysis scheme based on a block design with common references within each block for enabling large-scale label-free quantification. In this scheme, a large number of samples (e.g., >100 samples) are analyzed in smaller and more manageable blocks, minimizing instrument drift and variability within individual blocks. Each designated block also contains common reference samples (e.g., controls) for normalization across all blocks. We demonstrated the robu

SUBMITTER: Zhang T 

PROVIDER: S-EPMC7425200 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature