Table I

Proteins and their subcellular localization identified in peroxisomes and enriched peroxisomal membrane samples from mouse kidney by mass spectrometry-based proteomics methodologies

Numbers in parentheses represent total spectral counts of each group of proteins.

Intact peroxisomesPeroxisomal membranesTotal
SDS-PAGE/3D ion trapGPF(P+m/z)a 3D ion trapGPF(P+m/z)a LTQ-FTMSGPF(P+m/z)a LTQ-FTMSbSDS-PAGE 3D ion trapGPF(P+m/z)a LTQ-FTMS
Total number of MS/MS spectra searched42,32812,1068,8026,52028,2552,437100,448
Number of identified proteins1359110211413680252
Swiss-Prot annotation
    Number of proteins with known cellular localization11077849410664187
    Number of proteins with unknown localization25 (867)14 (73)21 (145)24 (176)32 (629)17 (93)65
    Number of known peroxisomal proteins47 (4,455)39 (832)49 (1,196)53 (1,759)47 (2,018)33 (328)64
        Peroxisomal matrix proteins34 (4,157)31 (736)39 (1,140)39 (1,70329 (1,529)24 (252)42
        Peroxisomal membrane proteins13 (155)8 (96)10 (56)14 (56)18 (489)10 (76)22
        Of these colocalized with other organelle8735818
    Number of mitochondrial proteins16 (198)10 (113)6 (59)7 (65)15 (118)9 (38)31
    Number of cytoplasmic proteins22 (444)10 (92)10 (85)10 (96)8 (61)5 (16)30
    Number of ER proteins4 (78)4 (38)4 (31)7 (45)14 (261)7 (35)27
    Number of proteins from other organelles13 (268)7 (24)8 (47)10 (18)11 (65)7 (36)35
Percentage of peroxisomal proteins (%)35434846354125
  • a Gas-phase fractionation in the m/z dimension for selection of precursor ions.

  • b Peroxisomal peak fraction analyzed in protein correlation profiling experiments.