Table II Comparison between the DeMix and MaxQuant workflow, with four database searching methods, based on the combined HeLa triplicate dataset
Search engineMaxQuantDeMix
AndromedaMascotMS-GF+ PercolatorMorpheus-AS
Peptide-spectrum matchesb1151351315977806380096118715193450122208200292
    PSM per MS/MS0.7140.8160.4840.4970.7361.1990.7581.242
Unique peptides3264638112231332309535468450223371241628
    PSM per peptide3.533.453.373.473.354.303.634.81
    Confetti supportedc86.4%84.6%89.3%89.4%85.4%83.0%86.3%84.6%
Protein groups44094642380038014831544347075167
    Strongly supportedd35973985286528683776444636914222
    Mean coverage24.4%25.1%22.9%22.9%24.7%25.7%24.6%25.6%
  • a Deconvolution: secondary peptides in MaxQuant or spectra cloning in DeMix are allowed (+) or not (-).

  • b PSM lists were trimmed to E-value < 0.05 for Mascot, or to FDR < 0.01 for Andromeda, MS-GF+ Percolator and Morpheus-AS.

  • c Proportion of unique peptide sequences found in the Confetti database (34).

  • d Protein groups supported by two or more unique peptides are considered to be strongly supported; and mean coverage was calculated for these strongly supported proteins.