Table II

TIF proteins

Protein nameMethod of identificationaSpot number in reference 2D gelsbPresence reported in plasma/serumcPresence reported in NAFdAccession numbereMALDI-TOF MSf
ScorePeptides and PSDCoverage
%
6-phospho-gluconolactonase (6PGL)MSIEF 1O953361501047
14-3-3 protein βMS, CKDIEF 2YesP319461201145
14-3-3 protein εMSIEF 3P4265598838
14-3-3 protein ηMS, CKDIEF 4Q049171301042
14-3-3 protein σMS, CKD, IBIEF 5Yes (1)P31947100940
14-3-3 protein ζ/σMS, CKDIEF 6Yes (1)P293121201548
1-309, T lymphocyte-secreted protein I-309AAP22362
37/67 laminin receptor, 40S ribosomal proteinMSIEF 7P0886580722
AAA ATPase p97MS, CKDIEF 8P55072921930
Actin-like protein 3, actin-related protein 3MSIEF 9P3239118514 (PSD: 1214.56 (266–275))31
Acylamino-acid-relising enzyme, oxidized protein hydrolaseMSIEF 10P13798801112
Acylaminoacyl-peptidaseMSIEF 11gi|2118063901115
Acyl-CoA-binding protein (ACBP), diazepam binding inhibitor (DBI)MSP071081087 (PSD: 1535.70 (1–13 N-Acetyl))40
Actin regulatory protein (CAP-G)MSP40012112011 (PSD: 11389.74 (307–319))37
AdenosylhomocysteinaseMSIEF 12Yes (1)P235261551735
AlbuminMS, IBIEF 13Yes (2)YesP027681451285
Alcohol dehydrogenaseMSIEF 14P145501201028
Aldehyde dehydrogenase 1MSIEF 15Yes (1)gi|2183299998 (PSD: 1540.71 (411–425))15
Aldehyde dehydrogenase 9MSIEF 16P49189801030
α 1 antichymotrypsinMSIEF 17Yes (3)YesP010111001022
α 1 protease inhibitorMSIEF 18Yes (1)P01009120816
α 1-B glycoproteinMSIEF 19Yes (2)P0421785614
α-actinin 4MSIEF 20Yes (1)O437071001011
α-centractinMSP42024931027
α soluble SNFattachment protein alpha (SNAP-α)MSIEF 21P549201701450
α-enolase, enolase 1MS, CKDIEF 22, NEPHGE 1P067331021125
α-tubulin 1 chainMS, CKDIEF 23P0520994818
Aminoacylase-1MSIEF 24Q031541001130
AngiogeninAAYes (1)P03950
Annexin IIB, CKDIEF 25P04083
Annexin IIIBIEF 26, NEPHGE 2Yes (1)P07355
Annexin IVCKDIEF 27P09525
Annexin VCKDIEF 28Yes (1)P08758
Apolipoprotein A-IMSIEF 29Yes (3)P026471501538
ATP synthase, α chainCKDNEPHGE 3P25705
ATP synthase, β chainCKDIEF 30Yes (2)P06576
ATP-dependent DNA helicase II, Ku autoantigen protein p86MSIEF 31P130101201916
B lymphocyte chemoattractant (CXC chemokine BLC)AAO43927
β actinMS, CKDIEF 32Yes (2)YesP02570802235
β tubulinCKDIEF 33P07437
BPNT1 proteinMSIEF 34gi|173895331411142
Brain derived neurotrophic factor (BDNF)AAP23560
Carbonic anhydrase 1MSIEF 38Yes (2)P009151381050
Cathepsin BIBP07858
%
Cathepsin DIB, MSYes (2)YesP073398810>22
CCG1-interacting factor BMSIEF 39Q96|U4807 (PSD: 1593.79 (9–22))27
Chaperonin containing TCP 1, subunit β (CCT-β)MS, CKDIEF 40P783711811535
Chaperonin containing TCP 1, subunit ε (CCT-ε)CKDIEF 41P48643
Chaperonin containing TCP 1, subunit θ (CCT-θ)CKDIEF 42P50990
Chloride intracellular channel protein 1MSIEF 43O00299110739
Chromosome 7 open reading frame 24MSIEF 44gi|13129018745 (PSD: 1253.71 (35–45))21
Chemokine β 8-1AAP55773
Coactosin-like proteinMSIEF 45Q14019129750
CofilinMS, CKDNEPHGE 4Yes (1)P2352895841
Collagen α 1 (VI) chainMSIEF 46Yes (1)YesP121091171520
Coronin like protein p57MSIEF 47Yes (1)P31146861020
Cyclin A/CDK2-associated protein p19MSIEF 48BP34991139950
Cyclophilin AMSNEPHGE 5P05092110637
Cyclophilin BMSNEPHGE 6P232841261243
Cytosol aminopeptidase, leucine aminopeptidaseMSIEF 49gi|126433941161125
E-CadherinMSIEF 50Yes (1)P12830907 (PSD: 1114.61 (216–224))9
Elastase inhibitorCKDIEF 51P30740
Elongation factor 1 α 1MS, CKDNEPHGE 7P04720931020
Elongation factor 1 βMSIEF 52P2453488732
Elongation factor 2 (EF-2)MS, CKDIEF 53Yes (1)P136392252630
Elongation factor 1-γ (EF-1-γ)MSP266411391228
EndoplasminCKDIEF 54Yes (1)P14625
Eosinophil lysophospholipaseMSIEF 55Q05315556 (PSD: 1026.60 (135–142))20
Eotaxin precursorAAP51671
Eotaxin-2AAYes (1)O00175
Eotaxin-3AAQ9Y258
Epidermal growth factor (EGF)AAYesP01133
Epithelial neutrophil-activating protein 78 (ENA-78)AAYes (1)P42830
Esterase DMSIEF 56P1076893723
F-actin cappling protein α-1 subunit, CapZ α-1MSIEF 57P5290770525
F-actin cappling protein β subunit, CapZ βMSIEF 58P4775680721
Fatty acid binding protein 5, epidermal (E-FABP)MSIEF 59Q014691501457
Fatty acid-binding protein, adipocyte (A-FABP)MSIEF 60P1509080625
Fatty acid-binding protein, heart (H-FABP), mammary-derived growth inhibitor (MDGI)MSIEF 61Yes (1)P0541380637
Ferritin light chain, L-subunitMSIEF 62Yes (1)P02792655 (PSD: 1491.7 (40–52))30
Fibrinogen β chain precursor (Contains: Fibrinopeptide B)MSYes (1)P0267516113 (PSD: 1032.33 (420–427))33
Fibroblast growth factor-4 (FGF-4)AAP08620
Fibroblast growth factor-6 (FGF-6)AAP10767
Fibroblast growth factor-7 (FGF-7)AAP21781
Fibroblast growth factor-9 (FGF-9)AAP31371
Filamin 1 (C-terminal part, degradation product)MSIEF 63P2133316018 (PSD: 1533.75 (442–455))26
Flt-3 ligand, Fms-related tyrosine kinase 3 ligandAAP49771
FractalkineAAP78423
Fructose-bisphosphate aldolase AMSNEPHGE 8Yes (1)P040751001245
Fumaryl acetoacetaseMSIEF 64Yes (1)P16930968 (PSD: 1273.66 (132–142))25
Galectin-1MS, IBIEF 65P093821001177
%
G-β 1 (Transducin β chain 1)CKDIEF 66P04901
G-β 2 (Transducin β chain 2)CKDIEF 67P11016
Gelsolin isoform bMSIEF 68Yes (1)Yesgi|38044288798 (PSD: 1244.58 (1–10))9
Gelsolin precursor, plasma (degradation product)MSIEF 69Yes (3)P063961071225
Glia maturation factor β (GMF-β)MS, AAIEF 70Yes (1)P17774102850
Glial cell derived neurotrophic factor (GDNF)AAP39905
Glucose-6-phosphate 1-dehydrogenaseMSIEF 71Yes (1)P114131161135
Glucose-regulated protein 75 (grp 75)MS, CKDIEF 72P386461331216
Glucose-regulated protein 78 (grp 78)MS, CKDIEF 73Yes (1)P110211401372
Glutathione S-transferase PMS, CKDIEF 74P092111971366
Glyceraldehyde 3-phosphate dehydrogenaseMS, CKDNEPHGE 9P003541751441
Glyoxalase 1 (GLO1)MSIEF 75Q0476094826
Granulocyte chemoattractant protein 2 (GCP-2)AAP80162
Granulocyte colony stimulating factor (GCSF)AAYes (1)Q99062
Granulocyte-macrophage stimulating factor (GM-CSF)AAYes (1)P04141
Growth-regulated oncogene (GRO)AAP09341
Haptoglobin 1MSIEF 76Yes (3)P007391702040
Haptoglobin 2 (N-terminal part)MSIEF 77Yes (1)P0073870715
Heat shock 70-kDa protein 4 isoformMSIEF 78Yes (1)P349329812 (PSD: 1495.69 (20–33))13
Heat shock protein 27 (hsp 27)MS, CKDIEF 79P04792109731
Heat shock protein 60 (hsp 60)MS, CDKIEF 80Yes (2)P108091231119
Heat shock protein 70 protein 2 (hsp 70)CDKIEF 81Yes (1)P54652
Heat shock protein 90 (hsp 90)MS, CDKIEF 82Yes (1)P079001992130
Heme binding protein 1MSIEF 83gi|20336761117641
Hemoglobin β chainMSIEF 84Yes (3)P020232121384
Hepatocyte growth factor (HGF)AAYes (2)P14210
Human epithelial mucin, Muc 1IBP15941
Immunoglobulin G light chain, κIBIEF 85, NEPHGE 10Yes (1)Yes
Immunoglobulin G heavy chainIBIEF 86, NEPHGE 11Yes (1)Yes
Importin β-1 subunit, Importin 90MSIEF 87Q149741011215
Initiation factor 3 subunit 2, (eIF3 p36)CKDIEF 88Q13347
Initiation factor 4D, eIF-4 DCKDIEF 89P10159
Insulin growth factor 1 (IGF-1)AAYesP01343
Insulin growth factor binding protein 1 (IGFBP-1)AAYes (1)P08833
Insulin growth factor binding protein 2 (IGFBP-2)AAYes (1)P18065
Insulin growth factor binding protein 3 (IGFBP-3)AAYes (2)YesP17936
Insulin-like growth factor binding protein-4 (IGFBP-4)AAP22692
Interferon γ (IFN-γ)AAP01579
Interferon-induced protein 10AAYes (1)P02778
Interleukin 1-α (IL-1 α)AAP01583
Interleukin 1-β (IL-1 β)AAYes (1)P01584
Interleukin 2 (IL-2)AAYes (1)P01585
Interleukin 3 (IL-3)AAP08700
Interleukin 4 (IL-4)AAYes (1)P05112
Interleukin 5 (IL-5)AAYes (1)P05113
Interleukin 6 (IL-6)AAYes (2)P08887
Interleukin 7 (IL-7)AAYes (1)P13232
%
Interleukin 8 (IL-8)AAYes (1)P10145
Interleukin 10 (IL-10)AAYes (1)P22301
Interleukin 12 (IL-12)AAYes (2)P29459
Interleukin 13 (IL-13)AAYes (1)P35225
Interleukin 16 (IL-16)AAYes (1)Q14005
Isocitrate dehydrogenaseMSIEF 90O758741281124
KAT proteinMSIEF 91gi|21636046112543
Keratin 19 (N-terminal part)MSIEF 92P0872790716
Keratin 10 (N-terminal part)MSIEF 93P13645801017
Lactate dehydrogenase B chainMSIEF 94Yes (2)YesP071952041638
Lactate dehydrogenase M chainMS, CKDNEPHGE 12P003381401525
LeptinAAYes (1)P41159
Leukemia inhibitory factor (LIF)AAYes (1)P15018
LIGHT, tumor necrosis factor ligand superfamily member 14AAO43557
LIM and SH protein 1MSIEF 95Yes (1)Q148471981648
L-plastinMS, CKDIEF 96Yes (1)P137962442542
Lyase adenylosuccinateMSIEF 97P305661081023
Lysophospholipase isoform 1MSIEF 98gi|5453722504 (PSD: 1271.66 (134–146))17
Lysolecithin acylhydrolaseMSIEF 99Q053151006 (PSD: 1439.32 (61–72))28
Macrophage colony stimulating factor (MCSF)AAYes (1)P09603
Macrophage inflammatory protein 1 βAAP13236
Macrophage inflammatory protein 1d (MIP-1d)AAQ16663
Macrophage inflammatory protein 3-α (MIP-3 α)AAP78556
Macrophage-derived chemokine (MDC)AAO00626
Malate dehydrogenaseMSIEF 100P409251311033
MaspinMSIEF 101P369521271031
Matrix metalloproteinase-1 (MMP-1)IBP03956
Matrix metalloproteinase-2 (MMP-2)IBYes (1)P08253
Matrix metalloproteinase-3 (MMP-3)IBP08254
Matrix metalloproteinase-9 (MMP-9)IBYes (1)P14780
Mesoderm inducing factor (MIF)AAP14174
Metastasin (S100 calcium-binding protein A4)IBP26447
Metastasis inhibition factor nm23, Nucleoside diphosphate kinase AMSIEF 102P15531927 (PSD: 1344.77 (7–18))40
MIG, γ interferon induced monokineAAQ07325
Monocyte chemoattractant protein 1 (MCP-1)AAP13500
Monocyte chemoattractant protein 2 (MCP-2)AAP80075
Monocyte chemoattractant protein 3 (MCP-3)AAP80098
Monocyte chemotactic protein 4 (MCP-4)AAQ99616
Neurotrophin 3AAP20783
Neurotrophin 4AAP34130
Neutrophil activating protein 2 (NAP-2)AAP02775
Neutrophil defensin 3 precursorMSIEF 103Yes (1)P59666824 (PSD: 1117.54 (80–88))20
NG-dimethylarginine dimethylaminohydrolase 2MSIEF 104968651731352
Nuclear matrix protein NMP200MSIEF 105gi|7657381100815
Nucleosome assembly protein 1-like 4MSIEF 106Q99733828 (PSD: 1336.64 (84–93))23
Nucleoside diphosphate kinase BMSNEPHGE 13P22392991061
Oncostatin MAAP13725
%
OsteoprotegerinAAO00300
PAI I (Endothelial plasminogen activator inhibitor)IBYes (1)P05121
Peroxiredoxin 1, natural killer-enhancing factor AMSIEF 107Q06830102828
Peroxiredoxin 2, thioredoxin peroxidase 1MSIEF 108Yes (1)P321192401445
Peroxiredoxin 3, antioxidant protein 1MSIEF 109Yes (2)P30048796 (PSD: 1206.68 (197–207))19
Peroxiredoxin 6MSIEF 110P300411098 (PSD: 1409.66 (41–52))37
Phosphoglycerate kinase (PGK)MS, CDKNEPHGE 14Yes (1)P00558811227
Phosphoglycerate mutase isomerase B (PGAM-B)MSIEF 111Yes (2)P186691501245
PIGFAAQ07326
Plasminogen activator inhibitor 2 (PAI-2)CKDIEF 112Yes (1)P05120
Platelet-derived growth factor BB (PDGF-BB)AAYes (1)P01127
Profilin IMS, CKDNEPHGE 15P07737142973
Progesterone membrane binding protein, steroid receptor protein DG6MSIEF 113O1517385622
Proteasome subunit alpha type 2 (C3)MSNEPHGE 16Yes (1)P2578794823
Proteasome activator 28-α (PA28 α)MSIEF 114Q0632310710 (PSD: 971.47 (191–198))40
Proteasome activator 28-β (P28 β)MSIEF 115O9UL46118930
Proteasome θ chainMSIEF 116P49720103815
Protein disulfide isomerase A3 precursorMSIEF 117Yes (2)P301011501327
Protein disulfide isomerase (PDI)MS, CKDIEF 118Yes (1)P072372351831
Psoriasin (S100A7)IBIEF 119Yes (2)P31151
Pulmonary and activation-regulated chemokine (PARC)AAP55774
Pyruvate kinase M2 isoformCKDNEPHGE 17YesP14786
Rab GDI βMSIEF 120P503951361436
Rab18MSIEF 121Q9NP72555 (PSD: 1216.62 (1–10 N-Acetyl))17
Rac 1CKDNEPHGE 18P15154
Raf kinase binding proteinMSIEF 122, IEF 123P30086100745
RantesAAYes (1)P15501
Retinoblastoma DEAE box proteinMSIEF 124Q92499741117
Retinoblastoma binding protein 4, retinoblastoma-binding protein p48MSIEF 125Q0902821361536
Retinoic acid-binding protein II, CRABP-IIMSIEF 126P293731901169
Rho GDP-dissociation inhibitor 1, Rho GDI 1MSIEF 127P52565103729
Rho GDP-dissociation inhibitor 2, Rho GDI 2MSIEF 128P52566103933
Ribonuclease/angiogenin inhibitor (RAI)MSIEF 129P134891481231
Ribosome binding protein 1, ribosome receptor protein (C-terminal part)MSIEF 130Q962E91453042
Rotamase, p59 proteinMSIEF 131Q027901091228
Selenium binding protein 1MSIEF 132gi|163065501091123
Serine/threonine phosphatase 2A, catalytic subunit αMSIEF 133P0532381622
Sertolli cell factor (SCF)AAP21583
SH3 domain-binding glutamic acid-rich-like proteinMSIEF 135O75368148967
Smooth muscle protein 22-α, SM22-αMSIEF 135Q019951701041
Spermidine synthaseMSIEF 136P1962385818
Stress induced phosphoprotein 1 (STI1)MSIEF 137P319481011528
%
Stromal cell-derived factor 1-α (SDF-1α)AAYes (1)P48061
Superoxide dismutase [Cu-Zn]MS, IBIEF 138Yes (1)P004412081256
Superoxide dismutase [Mn]MS, CKDIEF 139P04179100522
Synthetase glutamine-tRNAMSIEF 140P47897711216
ThioredoxinMSIEF 141P1059988858
Thrombopoetin (TRO)AAP40225
Thymidine phosphorylase precursor (TdRPase), platelet-derived endothelial cell growth factor (PD-ECGF)MSIEF 142P199711601221
Thymus and activation regulated chemokine (TARC)AAQ92583
Thyroid protein p24MSIEF 143Q139382081460
Tissue inhibitor of metalloproteinases-1 (TIMP-1)AAYes (1)P01033
Tissue inhibitor of metalloproteinases-2 (TIMP-2)AAYes (1)P16035
TransferrinMSIEF 144Yes (1)YesP027861301311
Transforming growth factor β 1 (TGF-β 1)AAP01137
Transforming growth factor β 2 (TGF-β 2)AAP08112
Transforming growth factor β 3 (TGF-β 3)AAP10600
TransketolaseMSIEF 145P294011001021
Translationally controlled tumor protein (TCTP)MS, CKDIEF 146P13693855 (PSD: 1241.66 (101–110))21
Transthyretin precursor, prealbuminMSIEF 147Yes (3)P02766757 (PSD: 1394.58 (56–68))44
Triosephosphate isomerase (TIM))MS, CKDIEF 148, NEPHGE 19P601741701969
Tropomyosin 1 α chain (N-terminal part)MSIEF 149P0949380930
Tropomyosin α 3 chainMS, CKDIEF 150Yes (1)P067532321440
Tropomyosin α 4 α chainMSIEF 151Yes (1)P072262402046
Tropomyosin 3/spliced isoform 2MS, CDKIEF 152PO6753–012401850
Tumor necrosis factor-α (TNF-α)AAYes (1)P01375
Tumor necrosis factor-β (TNF-β)AAYes (1)P01374
UbiquitinMS, CKDIEF 153P022481771085
Ubiquitin carboxyl-terminal hydrolase 14MSIEF 154Yes (1)P54578991526
Uroporphyrinogen decarboxylaseMSP061321721430
Vacuolar ATP synthase, catalytic subunit AMSIEF 155P3860690914
Vascular endothelial growth factor (VEGF)AAYes (1)P15692
Vimentin (degradation product)MSYes (1)P086703493347
WD-repeat protein 1, acting interacting protein 1MSIEF 156O7508370914
XAG-2, secreted cement gland homologMSNEPHGE 20gi|5453541104741
  • a MS, Identification of proteins separated by 2D gels using MALD-TOF MS; CKD, identification of 2D gel spots by matching the protein patterns to the master 2D gel keratinocyte database (proteomics.cancer.dk); IB, protein identification by Western 2D gel immunoblotting; AA, protein identification using cytokine-specific antibody arrays.

  • b The position of the identified proteins in the 2D gel is indicated with either an IEF (Fig. 2) or a NEPHGE number (Fig. 3). Proteins migrating in both directions are indicated with both an IEF and a NEPHGE number. A number of proteins exhibited multiple forms and some of them are underlined in Figs 2 and 3.

  • c Presence in the plasma/serum proteome (52): 1, identified by only one approach; 2, confirmed by identification using at least two approaches; 3, occurring in all four sets.

  • d Presence in the NAF proteome (35).

  • e The Swiss-Prot accession number is given for all identified proteins whenever the same peptides are recognized both in Swiss-Prot and NCBInr. Splice variants could not be distinguished in most cases due to the low amounts of starting material.

  • f For MALDI-TOF MS scores (Score) obtained from Mascot searches, the number of peptides (Peptides) recognized are indicated together with the mass and position of the peptides that were used for PSD analysis (PSD). The peptide sequence coverage is listed as a percentage of the entire protein sequence (Coverage).