Table I

Proteins identified from the lysosomal integral membrane protein fraction

The table is sorted by functional ontology. Protein name, NCBI accession number, and number of unique peptides identified are given.

Metabolism
    Aldehyde dehydrogenase 3-A2 13929028 2
    Apyrase 21426787 2
    Arachidonic acid epoxygenase 13929204 4
    Aryl sulfotransferase 1091600 1
    ATP synthase α subunit 6729934 4
    ATP synthase f0 β subunit 19705465 2
    ATP synthase F1 complex O subunit 20302061 3
    ATP synthase γ chain 39930503 3
    Betaine-homocysteine methyltransferase 13540663 5
    Carbamoyl-phosphate synthetase 1 8393186 2
    Catalase 6978607 2
    CYP2A1 6978741 3
    CYP2C13 25453406 1
    CYP2C22 19924039 2
    CYP2C29 9506529 1
    CYP2D2 6978747 1
    CYP4A3 28461155 2
    Cytochrome b5 11560046 5
    Dopa/tyrosine sulfotransferase 11968092 1
    Epoxide hydrolase 1 6978813 4
    Glyceraldehyde-3-phosphate dehydrogenase 8393418 1
    l-Gulono-γ-lactone oxidase 11560006 2
    Peroxiredoxin 1 16923958 3
    Retinol dehydrogenase type III 31377477 5
    Similar to NADH dehydrogenase (ubiquinone) 1 α subcomplex, 9 34858473 4
Immunity
    CD1 antigen 5420461 7
    Fc receptor 15375322 6
    Macrophage expressed gene 1 12018298 2
    MHC class I α chain 940825 1
    Polymeric immunoglobulin receptor 27151742 3
    Similar to Igh-6 protein 34935297 2
    Similar to immunoglobulin joining chain 34876693 3
Biosynthesis
    α-Mannosidase II 34877940 15
    Core 1 β-1,3-Galactosyltransferase 12621124 5
    Elongation factor Tu, similar to RIKEN cDNA 2300002G02 34859187 1
    Eukaryotic translation elongation factor 1 α-2 15805031 2
    Heat shock 70kD protein 5, GRP78, BiP 25742763 6
    Microsomal glutathione S-transferase 1 19705453 2
    N-Acetylglucosaminyltransferase I 13540685 6
    N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1; heparan sulfate-N-deacetylase/N-sulfotransferase 13242253 5
    ppGaNTase-T2 46877109 3
    Protein disulfide isomerase (ER60) 91897 1
    Ribophorin I 6981486 1
    Ribosomal protein L13 13592055 3
    Ribosomal protein L6 16758864 1
    Ribosomal protein L7, cytosolic [validated]–rat 11383729 2
    Ribosomal protein S3, cytosolic [validated]–rat 70850 1
    Ribosomal protein S3a, cytosolic [validated]–rat 8394221 1
    Ribosomal protein S4 227229 5
    Ribosomal protein S6 6677809 1
    Sialyltransferase 1 (ST6Gal1) 115446 13
    Sialyltransferase 4A (ST3Gal1) 6677957 2
    Sialyltransferase 8 (GT3 α-2,8-sialyltransferase) 6981540 1
    Similar to 60 S ribosomal protein L3 (L4) 38454246 1
    Similar to 60 S ribosomal protein L7a (Surfeit locus protein 3) (PLA-X polypeptide) 34853132 3
    Similar to 60 S ribosomal protein L8 27685597 3
    Similar to Heparan sulfate 2-sulfotransferase 34860929 2
    Similar to ribosomal protein S8 38049330 2
    Similar to Vesicular integral-membrane protein VIP36 precursor 27682691 6
    UDP glycosyltransferase 2 family, polypeptide B 13928718 1
    UDP-glucuronosyltransferase 2 family, member 5 34876712 1
Membrane receptors/Signaling and Cell adhesion
    Asialoglycoprotein receptor 1 7705290 3
    Asialoglycoprotein receptor 2 8392926 2
    Carcinoembryonic antigen-related cell adhesion molecule 13929060 2
    CD59 6978635 1
    Cell surface antigen RB13–6–rat 1363274 2
    E-Selectin ligand, Golgi apparatus protein 1 6677905 21
    Guanine nucleotide-binding protein α-11 subunit 13591951 1
    Harvey rat sarcoma oncogene, subgroup R 6677819 1
    Lipoprotein receptor-related protein 34865759 6
    OX47 111503 2
    p21/H-Ras-1 (c-H-ras) 131873 1
    Phosphatidylinositol 4-kinase type II 16758554 4
    Progesterone receptor membrane component 1 11120720 2
    Protein-tyrosine phosphatase, receptor type, F 9507013 2
    Purinergic receptor P2X4 13928806 4
    Rap2B 13386338 1
    Rras2, related RAS viral (r-ras) oncogene homolog 2 13399308 1
    Similar to Cux/CDP(1B1); Cux/CDP homeoprotein 34873366 1
    Similar to GTP-binding regulatory protein α-13 chain 34875240 1
    Similar to MEK binding partner 1 34860783 2
    Similar to pituitary tumor-transforming gene 1 protein-interacting protein 34852416 4
    Similar to ras-related C3 botulinum toxin substrate 1 isoform Rac1b 34870449 4
    Similar to RIKEN cDNA 1300006M19 34870394 1
    Similar to transferrin receptor protein 2 (TfR2) 34871536 3
    Toll-like receptor 3 33438238 10
Molecular transport
    ATP-binding cassette, sub-family B (MDR/TAP), member 6 18034785 3
    ATP-binding cassette, sub-family C (CFTR/MRP), member 2; Canalicular multispecific organic anion transporter; multidrug resistance associated protein 2 6978669 5
    Chloride ion pump-associated 55 kDa protein 21489987 1
    Niemann Pick C1 6679104 4
    Peptide/histidine transporter 21426791 1
    Similar to 2810423E13Rik protein 34856883 2
    Similar to calcium-binding mitochondrial carrier protein Aralar2 (Solute carrier family 25, member 13) (Citrin) 7657583 8
    Similar to MLN64 N-terminal domain homolog (STARD3 N-terminal like protein) 27686679 1
    Similar to Proteolipid protein 2 46485405 1
    Similar to putative protein, with at least 9 transmembrane domains, of eukaryotic origin (43.9 kDa) (2G415) 34863028 1
    Similar to Solute carrier 31, member 1 19424310 1
    Similar to Tm9sf1 protein 34874167 2
    Similar to transmembrane 9 superfamily member 2 34876089 2
    Similar to transmembrane 9 superfamily protein member 4 34859018 3
    Solute carrier family 25 (mitochondrial phosphate carrier; adenine nucleotide translocator), member 3; phosphate carrier, mitochondrial 20806141 1
    Solute carrier family 25, member 4; mitochondrial adenine nucleotide translocator 32189355 2
    solute carrier family 29 (nucleoside transporters), member 3 31745142 2
    vATPase 100kDa a3 subunit 7140942 3
    vATPase subunit B 17105370 2
    vATPase subunit D(V0) 3955100 9
    vATPase subunit D(V1) 40786463 3
    vATPase subunit E 1718091 1
    vATPase subunit G 27714615 1
    vATPase subunit H 14318722 2
    Voltage-dependent anion channel 1 6755963 4
Membrane structure and lipid rafts
    CD36 antigen-like 2 (LIMPII) 16758914 10
    DAMP-1 protein 37693510 2
    Flotillin-1 13124118 20
    Flotillin-2 13124119 15
    Golgi-associated protein GCP360 20302065 9
    LAMP1 6981144 10
    LAMP2 40254785 8
    Prohibitin 6679299 9
    Similar to band 7 protein (35.3 kDa) (4N53) 34863101 1
    Similar to Macrosialin (CD68) 34870966 3
    Similar to MAL2A 32693285 1
    B-cell associated protein 37; similar to repressor of estrogen receptor activity 34858436 8
    Stomatin (Erythrocyte band 7 integral membrane protein 7.2b) 7710018 8
Hydrolases/Co-factors
    5′ nucleotidase, ecto 11024643 2
    β-Galactosidase 192185 2
    β-Glucuronidase 8393510 2
    Cathepsin F 34861419 3
    Cathepsin L 67650 2
    Cathepsin Y 34328540 1
    Dipeptidylpeptidase IV 6978773 12
    GM2 ganglioside activator protein 48976085 2
    Kidney aminopeptidase M; Leucine arylaminopeptidase 1 13591914 2
    Lysosomal acid phosphatase 8392842 9
    Nicastrin 27819651 13
    Plasma glutamate carboxypeptidase 13928880 1
    Prosaposin 6981424 2
    Protective protein for β-galactosidase 6679437 3
    X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound 16924020 6
Secreted
    α-1-Inhibitor III 12831225 2
    α-2-HS-glycoprotein (fetuin) 6978477 7
    Apolipoprotein A-V 18034777 12
    Apolipoprotein b 34863099 4
    Apolipoprotein E 1703338 10
    Complement component 9 16924006 1
    Dermcidin precursor 16751921 5
    Epithelin/granulin precursor 8393493 4
    Ferritin light chain–rat 2119695 8
    Fibrinogen γ-A chain 71829 2
    Fibronectin 1 9506703 4
    Inter-α-inhibitor H4 heavy chain 9506819 5
    Peptidylprolyl isomerase C-associated protein (mama) 20806135 4
    Pregnancy zone protein 21955142 4
    Serum amyloid P 8392903 2
    Similar to cellular repressor of E1A-stimulated genes CREG 34880832 1
    Vitronectin 9507241 3
Unknown/Uncharacterized
        2810022L02Rik protein 15928581 1
    Expressed sequence AV006840 20846843 2
    Hypothetical protein XP_236205 34863318 2
    Mg87 protein 19705543 2
    RIKEN cDNA C730027E14 22122497 1
    Similar to Ab2–095 34865464 5
    Similar to apoptosis related protein APR-3; p18 protein 34862996 3
    Similar to cDNA 1810037C20 34881760 1
    Similar to CG14980-PB 34870407 2
    Similar to Chr14 ORF 34869712 3
    Similar to E25B protein 27701907 2
    Similar to FAM3C-like protein 38454280 1
    Similar to gray lethal osteopetrosis; gray-lethal 34853421 2
    Similar to HTGN29 protein; keratinocytes associated transmembrane protein 2 34870715 1
    Similar to hypothetical protein FLJ38482 34877746 2
    Similar to Hypothetical protein MGC18837 27719651 1
    Similar to hypothetical protein MGC29390 34869210 5
    Similar to hypothetical protein MGC40107 27672946 2
    Similar to RIKEN cDNA 1100001H23 34858551 3
    Similar to RIKEN cDNA 1110055L24 34854713 2
    Similar to RIKEN cDNA 2010320H07 gene 34853121 1
    Similar to TRIM14 α 34868472 7
    Unknown (protein for MGC:72560) 40018580 6
    Unknown (protein for MGC:72638) 40018550 1
Vesicular and protein trafficking
    Arl10C 12838871 4
    Cation-dependent M6PR 27713160 4
    Ergicp53, mannose-binding lectin 1 16758758 9
    Heat shock protein 8; Heat shock cognate protein 70; heat shock 70kD protein 8 13242237 5
    RAB11B, member RAS oncogene family 14249144 3
    Rab1A 4758988 7
    Rab2 13929006 1
    Rab5C 27689505 3
    Rab6 17512290 7
    Rab7 13027392 6
    RIKEN cDNA 1500016L11 21312151 3
    RIKEN cDNA 3930401E15 38083573 2
    Similar to ankyrin repeat hooked to a zinc finger motif long form 34873095 2
    Similar to EH-domain containing 1 34861835 1
    Similar to Golgi phosphoprotein 4; type II Golgi membrane protein; 130 kDa Golgi-localized phosphoprotein; cis Golgi-localized calcium-binding protein 34857091 6
    Similar to Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 34863597 2
    Similar to gp25L2 protein 34873639 1
    Similar to hypothetical protein
        5031407H10 34851786 2
    Similar to LRG-47 27670133 2
    Similar to NIPSNAP1 protein 34879019 2
    Similar to procollagen (type III)
        N-endopeptidase 34851987 1
    Similar to Rab18 27687387 1
    Similar to Rab5B 34862219 2
    Similar to RET-II 34867583 2
    Similar to RIKEN cDNA 2010012F05 34859075 2
    Sorting Nexin 3A 4507143 2
    SNAP α 2143586 2
    Syntaxin 7 11177920 4
    Syntaxin 8; syntaxin-like protein 3I35 13928908 4
    TGN38 20301976 6
    Ubitquitin 70637 5
    Vamp2B 4894188 2
    VAMP8 13929182 8
    Vesicle transport through interaction
        with t-SNAREs 1B homolog 34866243 3
    Vps24p protein272293081