DEqMS is a robust statistical method developed specifically for differential protein expression analysis in mass spectrometry data.
- limma: It assumes that proteins with similar abundance levels should have similar variances.
- DEqMS: a protein’s variance isn’t just about its abundance, but about how many measurements (peptides/PSMs) were used to calculate that abundance.
For instance, in limma, a protein quantified by 2 peptides and a protein quantified by 20 peptides are treated with the same statistical “weight” if their intensities are similar. DEqMS adds an extra layer: it models the variance as a function of the peptide count. It acknowledges that the 20-peptide protein is mathematically much more reliable (lower uncertainty) than the 2-peptide protein.
For more techical details, please refer to the original paper