Table 1 of
Allison, Mol Vis 2006;
12:655-672.Table 1 of
Allison, Mol Vis 2006;
12:655-672.
Table 1. Previously characterized proteins whose abundance was changed during thyroid hormone treatment in rainbow trout retina
Previously characterized proteins that were quantified and had greater than 50% change in expression level after thyroid hormone (TH) treatment. We report a T:C ratio, where T represents the abundance of the peptide in TH-treated retina, and C represents the abundance in the control retina. A T:C ratio represents the fold increase (if >1) or fold decrease (if <1) of the reported peptide in the retina of trout treated with TH. For proteins represented by multiple peptides (Table 3), the average fold change of all peptides is presented in brackets. Best confidence ("Best conf") and "Score" are indices that represent confidence in assigning mass spectrometry results to particular peptides, as defined in the Methods.
Best
Avg T:C Name Accession ID Peptide conf Score
------- -------------------------------- ------------ ----------------------------- ---- -----
27.914 Dissimilatory sulfite reductase gi|20501973 IKCAGCPDDCVASVAR 50 16
subunit A
24.369 Similar to double homeobox gi|30154764 NAAPGGVSPCSLVGR 75 20
protein
19.306 MLH1 gi|13517948 GEALCSISYVAR 75 20
19.306 Flavodoxin reductases gi|48785221 AANQTICVCCSR 75 20
19.306 Leucyl aminopeptidase gi|23475436 AAYVCGHVPVPR 75 22
15.033 Ubiquitination factor E4 gi|20384666 ECSFDSDNFK 50 15
(AAK33012, AY029484) omyk-59242
14.617 Probable RNA-directed DNA gi|7484429 DVCFRAAAHGGIALVDIK 50 16
Polymerase
14.320 Hyperglycemic hormone CHH-B gi|1078947 TLCLVVVMVASLGTSGVGGRSVEGVSR 50 16
14.320 ATPase, E1-E2 type family gi|22326934 EGEGIIGAIAISDCLRQDAEFTVAR 50 16
12.225 G-2 and S-phase expressed 1 gi|20127556 AVGSPLCVPARR 50 18
(GTSE-1)
11.057 Cyclin I [Q9Z2V9] ssal-10026 gi|9296967 AQMDSSQLIRCR 50 18
10.783 n-acylaminoacyl-peptide gi|6978512 ILVSCPQGSR 75 23
hydrolase (NP_036632, NM_012500)
omyk-63225
10.570 Putative ankyrin protein gi|12039395 CLCKHK 50 16
9.595 AGR_L_3383p gi|15891808 LSGHCRGGFFPAIDADGR 75 20
9.524 Tissue inhibitor of gi|31543867 RADSSCSWYR 50 16
metalloproteinase 2 (NP_035724,
NM_011594) ssal-5300
9.365 Histone macroH2A1.1 (AAC28846, gi|3395780 TVKNCLALADEK 75 20
AF058445) ssal-11335
8.973 Wpkci gi|13365599 LCILGGR 50 16
8.928 Transposase (AAL93203, AF486809) gi|19698551 QCLQCFAHTLQLVVGDGLK 50 16
omyk-55976
8.368 Growth differentiation factor 5 gi|4262327 TSQVKLFSCSTNR 75 23
precursor
7.858 E1B protein, large T antigen gi|1046213 CVCGK 50 16
6.523 ABC-type transporter homolog gi|11356557 CAAPDLAPGTGTIGKVTAHDPR 50 18
6.331 Fatty acid synthase gi|1345958 CPDLDYFVVFSSVSCGR 75 20
5.736 Citramalate synthases gi|23101987 ICAVLGR 75 20
5.359 Alpha-2-HS-glycoprotein gi|231467 LILFFCLAQLWGCR 50 16
precursor (Fetuin-A)
5.295 Similar to ethanol induced 6 gi|27708440 NCRPSR 50 15
4.542 emb gi|8953752 IGKDCHLGLMK 75 25
4.194 Long chain fatty acyl CoA gi|11466137 LTDAQHAECCNWYDGPTILQR 50 16
synthetase
4.097 Cytochrome P450 3A27 (O42563) gi|5921919 VCGYYLGR 50 16
omyk-66606
3.923 ps20 WAP-type four-disulfide gi|10198227 CPPPPRTLPPGACQAAR 75 22
core domain protein
3.786 F-box protein family gi|15231601 CLCNVLKR 50 16
3.652 AtaPKS3 protein gi|28170706 CAARFPAFGEALTVASASASGAVGIAVGR 50 18
3.611 Pyruvate dehydrogenase gi|1200524 RNPLDC 50 16
3.157 RB118 gi|22726343 VVCLHRIGR 50 16
2.994 NADH dehydrogenase subunit 8 gi|11466585 LCEAVCPAQAITIETESR 50 15
2.989 Immunoglobulin VH domain gi|4583873 LQESGGGLVQTGASLRLSCVASGR 50 16
2.974 Probable transposase gi|7521506 ACLGLLSLARR 50 18
2.770 Phosphotransferase gi|9628791 ECVFKSLLICNSVCLNHK 50 18
2.718 Solute carrier family 25 member gi|21105432 AGAREYNGLADCL 50 16
5 protein (AAM34660, AF506216)
ssal-19916
2.660 elongin C; transcription gi|5032161 TYGGCEGPDAMYVK 50 18
elongation factor B (SIII)
(NP_005639, NM_005648)
omyk-62584
2.549 RH2 opsin gi|30578194 GCMLATVGMK 75 24
2.337 flavocytochrome c flavin gi|24374580 LGACAVAEGVVTGRNAGR 50 18
subunit, putative
2.175 Unknown omyk-43180 ALACCAYGGK 75 25
2.135 Similar to AT motif binding gi|27659206 HNICKGR 50 16
factor 1
1.938 LWS opsin gi|20269378 TCIMQLFGK 99 39
1.934 Olfactory receptor MOR256-21 gi|18480540 LPFCPHHQVDDFVCEVPALIR 75 20
1.922 Calreticulin gi|1009712 SGSLFDNVLICDDPDYAKK 50 18
1.813 Putative nuclear protein, with a gi|17506383 ALCNVASRPR 50 17
coiled coil domain
1.807 4-Diphosphocytidyl -2C-methyl gi|22298148 TAEQVLIHDGARCLATPDLINR 50 15
-D-erythritol synthase
1.806 Glycosyltransferase GtfE gi|11263653 EDCFAIGEVNQQVLFR 50 16
1.794 Secreted gel-forming mucin gi|28865869 SPVTAPMTMSTSASAVTTSGCR 75 24
1.767 Polymorphic antigen P150 gi|7494470 CTSIQFHFDNYLK 75 22
precursor
1.753 Proteasome regulatory gi|18463069 ELEDHAECAAFSPATKLADR 50 16
non-ATP-ase subunit 5
1.753 Uridylate kinase gi|48764614 GIQVCLVIGGGNIFRGISTAAK 50 16
1.723 Putative transcription factor gi|584851 QACYKPLVDIACR 90 30
BOFH
1.723 Putative nuclear protein, with a gi|17539774 SAISDCVVSIRSSR 75 26
coiled coil-4 domain, nematode
specific
1.714 Transposase (CAB51372, gi|5579035 EFSLSMC 50 18
AJ249085) omyk-64012
1.707 Deoxyribonuclease gi|9629863 ALVRACCVPPGDLPTPDGLADGGGR 50 17
1.665 Calcium channel, gi|10864077 LLCRQEAVHTDSLEGK 50 16
voltage-dependent, alpha 1H
subunit
1.637 Transposase gi|15890093 ACLGIIRLVK 75 20
1.636 Neural cell adhesion molecule 1 gi|18859063 FFLCEVVGDAK 75 22
1.621 RacP67PHOX COMPLEX, Chain A gi|11513661 HHCPNTPIILVGTK 90 30
1.619 Similar to creatine kinase, gi|28856248 HNNCMASHLTPAVYAK 99 54
mitochondrial 1
1.605 WAP-type "four-disulfide core" gi|17538590 CVLNPKTEMGICCHQK 50 15
and thyroglobulin type-1 repeat
and antistasin family and Kunitz
1.585 Glycosyl transferases group 1 gi|17555286 CVGFLEGLCGK 50 16
1.582 CG15199-PA gi|24641213 LECTDDYLLLIR 75 21
1.582 3',5'-cyclic-GMP gi|108470 VFHLSYLHNCETR 99 40
phosphodiesterase
1.575 Tudor repeat 2 protein gi|38259208 SCTQCPQIGDPCIVR 75 20
1.568 Omyk-23419 gi|22001927 CFIVGADNVGSKQMQAIR 75 20
1.565 Ornithine decarboxylase gi|17432156 IIYAHPCK 75 22
1.561 3-hydroxyisobutyryl-coenzyme A gi|15239206 LDVIDRCFSR 50 16
hydrolase
1.529 SWS2 opsin gi|30578192 SCMMNLLGLK 90 28
0.676 Putative gag-pol polyprotein gi|37533472 CLHCKK 50 18
0.676 Oxysterol-binding protein-like gi|17529995 ACLPAPCPDTSNINLWNILR 75 21
protein OSBPL6
0.672 RNA polymerase beta-subunit gi|21702604 ACIAGHIGIMR 75 20
0.656 Phosphopyruvate hydratase gi|105934 ACNCLLLK 75 22
0.656 Putative nuclear protein family gi|17551954 LCGFECTNVR 75 25
member, with a coiled coil-4
domain
0.656 Similar to Cation transport gi|13473049 SLCVYSFVHRGTR 50 16
protein
0.656 Highly similar to triose gi|16801613 SSTSADANETCAVIR 75 23
phosphate isomerase
0.654 Solute carrier family 25 gi|16758854 CLLQIQASSGKNK 90 31
0.654 bsr5197 gi|27380308 ITGSSICDPLTSALPR 75 20
0.646 Upstream binding factor 1 gi|20955326 CYGRVTGTSK 50 16
0.642 Cytochrome P450 gi|21449376 ACIGRPFALQEATLVLALVLQR 50 16
0.639 1a protein gi|20087045 LWAIAGCDGR 75 22
0.639 Similar to immunoglobulin heavy gi|27669594 LTLGVCIPDVISRDLK 75 25
chain variable region
0.636 Group IIF secreted phospholipase gi|6174881 NSILSFVGYGCYCGLGGR 50 15
A2
0.633 dynamin-like protein MGM1 gi|485546 NKCHSTIEK 50 16
0.626 methyl coenzyme M reductase gi|15678482 SPSPGFNQRSCGGR 50 16
system, component A2 homolog
0.621 Arrestin gi|2308986 CAVEFEVK 75 24
0.615 26L protein gi|12085009 CTNDISSFLSEYK 50 16
0.611 yhbA gi|10955525 EVPAKWACIHK 75 20
0.610 60S ribosomal protein L37 gi|1350736 CSACAYPAARLR 50 16
0.610 Unknown (protein for MGC:59412) gi|28913682 RALLPPAACCLGCLAER 50 16
0.599 similar to proteasome subunit, α gi|20847133 IVEIDAHIGCAMSRLIADAK 75 22
type 5
0.597 PxORF80 peptide gi|11068083 LVFEEETCKDQIMSR 75 20
0.592 β tubulin gi|10242162 EIVHLQAGQCGNQIGAK 99 65
0.592 Rhodopsin gi|10720158 WIVVCKPISNFR 99 48
0.592 Myosin heavy chain gi|2104553 TYSGLFCVVVNPYK 75 21
0.590 guanine nucleotide-binding gi|11055998 LLLAGYDDFNCNVWDTLK 90 32
protein, β-4 subunit
0.588 Oxidoreductase, aldo gi|15643766 GPEVSAIGLGCMR 75 20
0.587 bikunin gi|17566852 AAKCPGDHVCTPR 50 18
0.586 Uridylyltransferase gi|17934262 ADGSGIDCARR 75 23
0.580 SOX-20 protein gi|4186021 SSGAGPSRCGQGR 50 18
0.577 7 transmembrane chemoreceptor gi|17566844 GLIDMFRCHK 50 18
family member
0.577 Pantetheine-phosphate gi|28493532 GLLVDCCK 75 22
adenylyltransferase
0.574 Quercetin 3-O-methyltransferase gi|24212064 YLTKNQDGVSIAALCLMNQDK 75 20
1
0.570 Thyroglobulin gi|13591876 DNFACVTSDQEEDAVDSLK 50 18
0.567 CG6562-PB gi|18497296 IVACGANYGVFHASNGQVLR 50 16
0.566 Diadenosine tetraphosphatase gi|15615408 TAYYVPGNHCNKLYR 50 16
0.551 (S)-2-hydroxy-acid oxidase chain gi|30019448 NTNEVAEVLKVCNTHK 50 18
D
0.551 Δ A gi|18858541 NNRYVCACVSGYGGR 75 20
0.551 3-methyladenine DNA glycosylase gi|46164618 FVDAAFAAFCTRNPLR 50 16
0.551 Undecaprenyl-PP -MurNAc- gi|33866863 LLGRFCGAVAVGLPAAAGR 50 16
pentapeptide -UDPGlcNAc GlcNAc
transferase
0.526 Hyaluronan and proteoglycan link gi|30102948 YPVVHPHPNCGPPEPGVR 90 28
protein 3
0.525 Major royal jelly protein 2 gi|20138892 WLFMVACLGIACQGAIVR 50 18
precursor (MRJP-2)
0.518 exo-1,4-beta glucosidase gi|1016746 CVEHEVSEAQAAIITIGRQAGEGLDR 75 20
0.517 ATP-dependent DNA helicase gi|21233561 IRGDGADGLTICTFHALGLK 75 24
0.513 ATP-dependent DNA helicase gi|15924217 VGRSDQQSYCVLIASPK 75 26
0.503 AP2 domain protein RAP2.2 gi|18400321 MCGGAIISDFIPPPRSLR 50 17
0.503 Clusterin precursor (P14018) gi|1705937 CVAIQDIDCSGKKPLTGPLK 50 16
ssal-1835
0.501 P0686C03.10 gi|28201266 ENPGVVSEALFALSCGPDLRVK 50 16
0.498 transcriptional regulator, MerR gi|21229272 IEGILQGACR 75 20
family
0.487 C20orf92 protein gi|18592788 RPCPSPEPGGR 50 16
0.485 β tubulin gi|1220547 GHYTEGAELIDSVLDVCR 99 66
0.472 CG14768-PA gi|20129709 CPSPGLRPEPQSPTIARPQK 50 16
0.468 Protease subunit of gi|48849255 VSTVCIGQAASMGSFLLAAGEPGMR 50 16
ATP-dependent Clp proteases
0.459 876aa long hypothetical gi|15921715 AVCKLYDK 50 16
DNA-directed DNA polymerase
0.424 Unknown omyk-43142 VKMCIYLR 50 18
0.418 Yts1F protein [Yersinia gi|27529238 CAIKYWR 50 16
enterocolitica (type 0:8)]
0.414 acetyltransferase, GNAT family gi|16126448 MRINACWPLGAPDR 50 16
0.409 Unknown omyk-41466 IGALGCLCSDVSRLVK 50 16
0.379 Recombinational DNA repair gi|23469354 CQVFITCVDQEFLR 75 24
ATPase
0.367 ferredoxin-like protein gi|39648848 LACQCFVR 50 18
0.362 UDP-glucose 4-epimerase gi|23104908 NGSAESLARVAAICGR 75 20
0.352 NAD-dependent aldehyde gi|23472045 CWIEAGLPAGVLNLLQGGR 50 15
dehydrogenases
0.337 Zinc finger protein 304 gi|27500786 IHTGERPYGCEVCGR 50 16
(XP_065054, XM_065054)
ssal-18954
0.302 Probable transport transmembrane gi|17545137 ASLWLDRVSGCIFIGLGLR 50 16
protein
0.295 Fibroblast growth factor gi|596009 KPLKGQTDGYIVVYCLK 50 18
receptor precursor
0.291 Similar to hypothetical protein gi|20864596 CVVCREAFPNAVALR 75 24
FLJ38281
0.287 Polyprotein gi|1030731 SNVTCYRCGQPGHFSNQCPK 50 16
0.286 Peroxiredoxin 2 family protein gi|15676839 AQESVAIFTKPGCQFCAK 50 18
0.268 3-oxoacyl-(acyl-carrier-protein) gi|17548579 LACPLPAFEVPATYPR 50 18
synthase II
0.264 Muscarinic receptor 5 gi|18409573 ALLRSCFSCPHPTLVQR 50 17
0.264 lysozyme gi|11342495 ISQEGLEHLIDCEGCKR 50 15
0.261 Arginine decarboxylase gi|17224235 IGLEAGSKPEILMAMGCLCK 75 22
0.251 Unnamed protein product gi|12860185 TCLAGFSPDGLLNVCQR 50 18
(BAB31871, AK019829)
oner-29064
0.242 Inner mitochondrial membrane gi|16716421 CFKAFCK 50 16
peptidase 2-like
0.238 Adenylosuccinate synthetase gi|18976680 CAIIEPKHK 50 17
0.237 Germination protein gi|23097938 SNEIAINGLLDGYCLLIK 50 16
0.237 a372L gi|9631940 LYIRGMCR 50 16
0.227 Similar to 60S ribosomal protein gi|27715587 QAVLCLPPGCALRALGR 50 16
L9
0.225 inositol 1,4,5-triphosphate gi|9910290 CVVQPDAGDLANPPKK 50 15
receptor 2 (NP_064307,
NM_019923) ssal-9833
0.209 Lipid transfer protein gi|21591782 CLVGAANSFPTLNAAR 50 16
0.208 Envelope protein E1 gi|402450 HQTVQTCNCSLYPGHVSGHR 75 20
0.202 LmbE homologs gi|23104913 GPRTSNCAIPSAAPIANTR 50 16
0.201 Ring finger protein 150 gi|51464218 LACDPNTKFAAPTR 50 16
0.185 Histidinol-phosphate gi|14520265 GILVRDCTSFGLPGYIR 50 18
aminotransferase
0.185 Nucleic-acid-binding protein gi|48780774 ALCSECQSLDLNWLDSDRR 75 20
containing a Zn-ribbon
0.182 Dimethyladenosine transferase gi|46192173 DARCLPALAEVAAAWPGR 75 22
0.180 Arp2 gi|11359368 VVEVAGLGCIGR 50 18
0.179 Guanylate nucleotide binding gi|23956350 CFVFDAPALGSK 50 15
protein 5
0.174 hypothetical protein MGC28149 gi|22122731 AINPLGEDVVECTLLVR 75 21
(NP_666301, NM_146189)
omyk-23548
0.174 pyruvate kinase gi|15789598 FRPSVPVVCATPSHDVR 75 26
0.172 IgiA gi|5852323 LCAEQALAALPLTAAVLGR 50 19
0.170 enterobactin synthetase, gi|17988425 GCAIAVAARQSR 75 22
component D
0.167 Phytochrome A type 3 (AP3) gi|130181 YACEFLAQVFAVHVNR 50 19
0.164 NADPH--ferrihemoprotein gi|85592 EQGKEVGETVLYCGCR 75 22
reductase (A28577) omyk-57898
0.159 Dual specificity phosphatase and gi|51491914 ALSDDHSKILVHCVMGR 50 16
pro isomerase domain containing
1
0.144 Cytosine-5-methyltransferase gi|28872780 NCFLPLREYFK 50 18
3-like protein isoform 2
0.138 Hypothetical protein gi|22980883 VVCNNTLQIALGR 50 16
0.129 Envelope glycoprotein gi|13559470 CVTPNCTDWK 50 16
0.125 Similar to Protein kinase PKX1 gi|30155809 EVIRPFLICVLK 75 24
0.124 β-globin (BAA11632) omyk-21057 gi|1183021 LLADCITVCVAAK 75 20
0.120 Phosphoenolpyruvate synthase gi|21231605 LCAENGGGEVAVAVR 50 16
0.118 Similar to heparan sulfate gi|27707418 ITAASAGGLEDSSFLCR 50 16
6-O-sulfotransferase 2 isoform S
0.116 Putative Na+-dependent inorganic gi|4895179 CAAEGVLTGGGGSEAIAEVR 50 16
phosphate cotransporter
0.110 β-tubulin gi|4210476 GRSCTVQAGQCGNQIGAK 75 22
0.104 protein kinase gi|27462493 AGVCTGFKCHK 75 22
C-zeta-interacting protein
0.096 GTP-binding protein -related gi|15222829 CFSSKVSMSLK 50 16
0.081 Insulin receptor-related gi|112516 CVTAESCANLRSVPGR 50 15
receptor precursor
0.071 c-myc gene single strand binding gi|4506447 CDAVIAHFNGKFIK 50 16
protein 2 omyk-46240
0.061 T-complex protein 1 gamma gi|6318665 IEKIPGGAIEDSCVLEGVMFNK 50 18
subunit
0.060 Non-selenium glutathione gi|6689393 CVFVIGQDK 50 18
phospholipid hydroperoxide
peroxidase (CAB65456, AJ243849)
ssal-71537
0.055 Thioredoxin reductase gi|48787275 IGSLPNVSLCTR 75 26
0.053 Unknown ssal-68895 TGCHLVAGR 50 18
0.050 chloroplast gi|13937285 CPVSVSLIAR 75 21
protein-translocon-like protein
0.047 Unknown ssal-28398 LVYIVCCK 50 16
0.040 KIAA0296 gene product gi|41281441 QLSSHICAHLR 50 16
(NP_055514, NM_014699)
omyk-42104
0.040 Unknown ssal-13231 VFCCSLVR 50 18
0.028 Unknown omyk-49337 CHPLLRCSPR 50 16
0.005 hypothetical protein gi|11360273 CVGHNGRTLAHESCNPK 50 18
DKFZp762C1110.1 (T47158)
ssal-8353
|