Table II Search results on the Yeast data set for MixDB, M-SPLIT, InsPecT, and ProbIDtree. (a) Numbers of identified spectra (single-peptide and mixture) and unique peptides are compared. (b) To allow for identification of co-eluting peptides, all searches were run using 3 Da precursor mass tolerance. The accurate precursor mass information was then used a posteriori to estimate the precision of peptide identification by comparing the theoretical precursor m/z of peptides returned by each method and the observed precursor m/z values in the corresponding MS1 scan (isotopic profile). An identification is considered correct if the difference between theoretical and experimental precursor m/z values is less than 5 ppm. For mixture spectra the precision is slightly lower because the second peptide in the mixture is usually of low-abundance (average α = 0.3) and thus harder to identify
a) Spectrum and peptide identifications in the Yeast dataset
Spectrum IdentificationsUnique Peptides
Single-peptideMixtureTotalSingle-peptideMixtureTotal
MixDB2393097824908547611285802
ProbIDtree198408212066044208204739
InsPecT22658n/a226585272n/a5272
M-SPLIT28417256730984599723946684
Methodb) Estimated precision in the Yeast dataset
Single-peptide matchesMixture matches
MixDB98.3%95.9%
ProbIDtree97.8%90.1%
InsPecT97.1%n/a
M-SPLIT97.3%95.4%