Table II Overview of analyzed DIA libraries. The names of each library consists of the spike-in types (MM: master mix, i.e. mixture of background and spike-ins in fixed amount, GS: gold standard, i.e. the same samples as measured by DIA), the digest type (IS: in-solution, F: fragmented and therefore in-gel), whether fractionation was performed and on which level (Prot: protein fraction, Pep: peptide fractionation), finally, the number represents the number of MS runs for the library. The libraries generated by Pulsar instead of ProteomeDiscoverer are indicated by the respective prefix
NameSpike-in typeDigest typeFractionationNo of runsSoftware
MM IS 6ConstantIn-solutionNo6PD+SN11
GS IS 15VaryingIn-solutionNo15PD+SN11
GS IS 30VaryingIn-solutionNo30PD+SN11
MM F Prot 20ConstantIn-gelProtein20PD+SN11
MM F Pep 16ConstantIn-solutionPeptide16PD+SN11
IS and F all 78CombinedCombinedCombined78PD+SN11
Pulsar GS IS 15VaryingIn-solutionNo15SN Pulsar
Pulsar MM F Prot 20ConstantIn-gelProtein20SN Pulsar