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

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 platform reached a fully satisfactory
quality of measurements at low-abundance ranges. PD methods including
normalization were the most accurate in estimating the abundance ratio
between groups and the most sensitive when comparing groups with a
narrow abundance ratio; on the contrary, MQ methods generally reached
slightly higher specificity, accuracy, and precision values. Moreover,
we found that applying an optimized log ratio-based threshold can
maximize specificity, accuracy, and precision. Taken together, these
results can help researchers choose the most appropriate MS1-based
protein quantification strategy for their studies.