Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-Based Protein Quantification Tools.

ABSTRACT: MS1-based label-free quantification can compare precursor ion peaks across runs, allowing reproducible protein measurements. Among bioinformatic platforms enabling MS1-based quantification, MaxQuant (MQ) is one of the most used, while Proteome Discoverer (PD) has recently introduced the Minora tool. Here, we present a comparative evaluation of six MS1-based quantification methods available in MQ and PD. Intensity (MQ and PD) and area (PD only) of the precursor ion peaks were measured and then subjected or not to normalization. The six methods were applied to data sets simulating various differential proteomics scenarios and covering a wide range of protein abundance ratios and amounts. PD outperformed MQ in terms of quantification yield, dynamic range, and reproducibility, although neither

SUBMITTER: Palomba A 

PROVIDER: S-EPMC8280745 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature