Table II

Proteomics data for all analyzed protein spots and comparison with corresponding mRNA expression

ProteomicsGene symbolDNA chip hybridization
Spot IDpH gradientFold regulation T47D-r versus T47DGenBank protein identifierIdentified proteinMr theor.Mr exp.pI theor.pI exp.Matched pept./total pept. in digest1Error2seq. cov.GenBank nucleotide identifierT47D-r versus T47D
HuGeneFL 1. Exp.HuGeneFL 2. Exp.Hu95A
kDakDappm%
Not present on chip
         3pH 4–76.3gi 12652557gi 13569956Similar to actin related protein 2/3 complex, subunit 517156.26.34 /53933NM_030978np4npnp
         6pH 4–71.5gi 4406577Unknown, clone 2495219145.25.47 /1051436AF131758npnpnp
        33pH 4–7−2gi 60184586-phosphogluconolactolase28255.75.911 /123049PGLSAJ243972npnpnp
        56pH 6–11only in T47D-rgi 107356gi 131528Polypyrimidine tract-binding protein PTB1 or PTB257589.38.74 /4228PTB2, PTB1X66975npnpnp
        57pH 6–111.857589.38.75/61810
        58pH 6–112.157589.38.76 /61112
        67pH 5–8−3.3gi 6164955Vacuolar sorting protein VPS29/PEP1121256.37.25 /51832VPS29NM_016226npnpnp
        73pH 5–83.9gi 4680711CGI-36 protein19276.47.29 /112033NM_015963npnpnp
Regulation data not well-defined on mRNA level
        16pH 4–7−1.7gi 3024348Platelet-activating factor acetylhydrolase26255.65.85 /82123PAFAH1B2D63390npnp1
        26pH 4–7−2.3gi 4759212Beta-tubulin cofactor13115.35.16 /91143TBCAAF038952npnp−1.5
        35pH 4–7−2.1gi 4506203Proteasome subunit30267.86.08 /121323PSMB7D380481.11.3−1.1/−1.2
        37pH 4–7−2.3gi 4506003Protein phosphatase 1 alpha isoform38395.96.216 /241649PPP1CAS57501npnp−1.2
        47pH 6–112.9gi 45053994-nitrophenylphosphatase domain and non-neuronal SNAP25-like 133249.58.412 /142326NIPSNAP1AJ001258npnp−1.1
        48pH 6–112.7gi 4507791Ubiquitin-conjugating enzyme E2M21177.77.27 /81435UBE2MAF075599npnp1.8
        49pH 6–112.46gi 4505591Peroxiredoxin 1, proliferation-associated gene A (natural killer-enhancing factor A)22198.77.719 /222064PRDX1X67951npnp1
        53pH 6–112.2gi 5454064SYT interacting protein70809.78.716 /241626RBM14AF080561npnp−1.2
        54pH 6–113.870809.78.710 /122217
        55pH 6–112.170799.78.79 /121216
        68pH 5–82.3gi 3859560Acyl-protein thioesterase25296.87.56 /91228LYPLA2NM_007260npnp1.3
        72pH 5–82.1gi 509033GARS protein47556.37.110 /13930GARSX54199undef71.11.2
        74pH 5–8only in T47D-rgi 547753Keratin, type II cytoskeletal 458606.37.29 /141719KRT4X07695undefundef1.3
Inverse regulation on protein and mRNA level
         4pH 4–7−2.9gi 238470 gi 251370Acid phosphatase isozyme Bf or Af18147.16.412 /141481ACP1U258491.41.7−1.1
        27pH 4–7−2gi 4827038gi 1706289Tumor protein D5220224.95.06 /681438TPD52U18914undef<1.31.2
        34pH 4–7−6.2gi 1352435Eukaryotic translation initiation factor 4E25255.86.06 /73122EIF4EM153531.1−1.11.5
        45pH 6–11−2.3gi 4507777Ubiquitin-conjugating enzyme E2D 317128.07.38 /11934UBE2D3U393182.21.21.5 /1.3
        60pH 6–11only in T47D-rgi 4504327Hydroxyacyl-Coenzyme A dehydrogenase52579.68.79 /102521HADHBD16481−1.2−1.2−1.4
        61pH 6–115.152579.68.715 /181835
        62pH 6–116.252579.68.814 /152635
        63pH 6–111.6gi 4758504Hydroxyacyl-Coenzyme A dehydrogenase, type II27228.07.115 /172075HADH2U73514<−1.6−1.5np
        64pH 6–111.627218.07.15 /62017
        65pH 6–11−2.5gi 5902074Stromal cell-derived factor 223217.27.16 /73135SDF2D506451.4−1.1−1
        66pH 5–8−2gi 4506195Proteasome subunit, beta type, 223286.57.413 /181150PSMB2D265991.71.21.1
Regulated in parallel on mRNA and protein level
1pH 4–7−3.6gi 999882Cellular retinoic acid-binding protein II16115.45.616 /201482CRABP2M97815>−2.5−2.8−1.6
7pH 4–71.5gi 2392338Glyoxalase I21205.15.010 /141451GLO1D133151.41.61.2
kDakDappm%
9pH 4–71.621205.15.19 /142039
8pH 4–71.5gi 4502969Catechol-O-methyltransferase30215.35.112 /191847COMTZ26491M585252.1>2.31.9 −1.1np2.2
12pH 4–7−9.3gi 2281474BCSG1 protein (synuclein-gamma, breast cancer-specific protein 1)13125.44.88 /111438SNCGAF010126npnp−2.2
13pH 4–7−11.8gi 229383Cytochrome b5 fragment10135.24.85 /6575CYB5L39945M22976np−1.3np−3.4−2 undef
14pH 4–7only in T47Dgi 4503143Cathepsin D45276.16.310 /121422CTSDM63138<−7.5−4.3−7.3
17pH 4–7−22.945266.15.811 /14626
20pH 4–7only in T47D45266.15.46 /72013
21pH 4–7−5.945276.15.410 /101124
32pH 4–7−2.145276.15.25 /7288
69pH 5–8only in T47D45366.16.813 /18838
15pH 4–7−6.6gi 4758984RAB 11A24196.15.95 /8321RAB11AAF000231−1.8−2.8−2.3
18pH 4–74.2gi 1421662Annexin A336325.65.716 /18941ANXA3L20591 M205603.7 np1.7 npnp 7.5
19pH 4–77gi 4557032Lactate dehydrogenase B37365.75.910 /111327LDHBX13794undef>101.1
22pH 4–7−3.2gi 15295949Hypothetical protein FLJ1361227295.35.412 /1481959NM_025202npnp−4.4
23pH 4–7only in T47D27275.34.74 /41417
25pH 4–7−7.89gi 227920Beta galactoside soluble lectin1575.35.08 /121254LGALS1J04456−1.6−1.6−1.9
38pH 4–7−2gi 387010Pyruvate dehydrogenase E1-beta subunit precursor37365.45.613 /191144PDHBD900861.1−1.6−1.9
39pH 4–73.5gi 4758904Serine protease inhibitor 643445.25.412 /181232SERPINB6S692721.52.91.5
42pH 4–75.6gi 4505291MxA/p7876945.65.923 /251132MX1M33882>8.7>5.2>3.6
43pH 4–7276945.65.820 /221129
44pH 6–11−2.9gi 5453541Anterior gradient 220139.08.410 /111250AGR2AF038451npnp−5.3
46pH 6–11−19.1gi 4557337Argininosuccinate synthetase47508.57.511 /142023ASSX01630−1.3−5−3.1
52pH 6–112.5gi 2624694Chain A, human mitochondrial single-stranded DNA binding protein15118.27.912 /141879SSBP1M945561.61.31.2
70pH 5–8−4.1gi 4557587gi 31291Fumarylacetoacetase47506.57.28 /101425FAHM55150−1.9−1.4<−2
71pH 5–8only in T47Dgi 5729980Phosphomevalonate kinase22265.66.313 /141635PMVKL77213−1.4−1.7−1.9
Regulated up and down on protein level
2pH 4–7−2.2gi 5031851Stathmin17145.85.810 /145450STMN1M313031.41.41.4
5pH 4–73.617145.85.54 /65925
10pH 4–72.1gi 601683814–3-3 protein gamma28254.84.811 /16545YWHAGABO24334npnpnp
11pH 4–7−2.628254.84.810 /13936
24pH 4–73gi 6694937gi 6288769Adenosine 5′-diphosphosugar pyrophosphatase25284.94.96 /82327NUDT5AF218818npnpnp
28pH 4–72.425304.94.87 /881529
29pH 4–7−225374.94.74 /42514
  • 1 Autolytic tryptic peptides and contaminants were not taken into account.

  • 2 Average error of matched peptide masses.

  • 3 Two peptides confirmed by electrospray ionization MS/MS.

  • 4 np, Not present on array.

  • 5 One peptide confirmed by MALDI-post-source decay.

  • 6 Spot saturated.

  • 7 undef, Undefined, indicating that in the two compared chip hybridizations no signal was detected.

  • 8 One peptide confirmed by electrospray ionization MS/MS.

  • 9 Spot partially in gel front.