Table IV

Detail of overlapping protein identifications by algorithm

Algorithm(s)Number of proteins
Number of proteins with one or more distinct peptides
    Found by all algorithms1,671
    X! Tandem128
    OMSSA573
    Sequest83
    Mascot82
    X! Tandem and OMSSA116
    X! Tandem and Sequest8
    X! Tandem and Mascot16
    OMSSA and Sequest100
    OMSSA and Mascot42
    Sequest and Mascot5
    X! Tandem, OMSSA, and Sequest45
    X! Tandem, OMSSA, and Mascot98
    X! Tandem, Sequest, and Mascot7
    OMMSA, Sequest, and Mascot80
    Total proteins discovered3,054
Number of proteins with two or more distinct peptides
    Found by all algorithms1,090
    X! Tandem47
    OMSSA405
    Sequest10
    Mascot15
    X! Tandem and OMSSA76
    X! Tandem and Sequest2
    X! Tandem and Mascot5
    OMSSA and Sequest54
    OMSSA and Mascot24
    Sequest and Mascot2
    X! Tandem, OMSSA, and Sequest45
    X! Tandem, OMSSA, and Mascot79
    X! Tandem, Sequest, and Mascot2
    OMMSA, Sequest, and Mascot53
    Total proteins discovered1,909