Dengjel et al. Mol. BioSyst., 2010, Supplementary Material (ESI) for Molecular BioSystems DOI: 10.1039/c003962d This journal is (c) The Royal Society of Chemistry, 2010 Supplementary Table 1: Fibroblast control. Cell lysates were prepared from unlabled (Arg0/Lys0) and labled (Arg10/Lys8 fibroblasts after 14 cell doublings in culture (D14). Shown are normalized log2 transformed protein ratios of identified protein identification a minimum of 2 peptides per protein has to be identified (unique + razor). The database used for identification decoy database based on IPI v. 3.59 containing in total 160,820 entries. As a criterium for identification the posterior errror probaility rate of identified proteins (PEP) is shown. The peptide numbers represent peptides used for quantitation. Unique + Razor Sequence Peptide Variability Protein ID Gene Symbol Coverage [%] PEP Log2 Ratio No. [%] Quantil IPI00021033; COL3A1 11.1 5.91E‐62 ‐4.651 4 165.2 Q1 IPI00761105; TADA2B 1.7 2.46E‐02 ‐4.494 2 57.9 Q1 IPI00152007 ARHGEF17 2.3 5.41E‐09 ‐3.687 2 92.5 Q1 IPI00300725;C KRT6A 27 6.82E‐61 ‐3.299 4 204.0 Q1 IPI00022229; APOB 0.7 5.68E‐29 ‐2.944 8 202.2 Q1 IPI00298860; LTF 51 8.02E‐197 ‐2.834 13 105.6 Q1 IPI00384444; KRT14 36.4 6.18E‐85 ‐2.542 13 143.3 Q1 IPI00305461; ITIH2 5 2.86E‐09 ‐1.174 3 367.3 Q1 IPI00420088; KIAA0174 7.5 9.34E‐03 ‐0.892 2 62.3 Q1 IPI00012887; CTSL1 12 3.13E‐21 ‐0.618 3 47.8 Q1 IPI00375714; HSPB7 17.1 1.31E‐05 ‐0.615 2 69.5 Q1 IPI00384140 ESR2 10.6 4.35E‐04 ‐0.551 3 8.6 Q1 IPI00300599; CTSK 46.5 <1.0E‐304 ‐0.515 9 11.7 Q1 IPI00167949; MX1 18.3 7.22E‐90 ‐0.508 8 13.1 Q1 IPI00848334; KIF2A 8.5 3.58E‐39 ‐0.467 2 33.7 Q2 IPI00296534; FBLN1 18.2 2.50E‐34 ‐0.462 4 25.3 Q2 IPI00296713; GRN 3.9 1.10E‐14 ‐0.455 2 9.9 Q2 IPI00297646;C COL1A1 46.7 <1.0E‐304 ‐0.419 58 49.1 Q2 IPI00749429; TTYH3 2.7 8.52E‐48 ‐0.406 2 8.3 Q2 IPI00026111; TMCO1 12.2 1.52E‐38 ‐0.389 2 20.8 Q2 IPI00027780; MMP2 17.7 7.88E‐76 ‐0.383 8 12.4 Q2 IPI00384280; PCYOX1 35.4 1.98E‐191 ‐0.377 8 18.9 Q2 IPI00873137; COL1A2 36.9 <1.0E‐304 ‐0.370 38 24.9 Q2 IPI00100199; CYBRD1 7.7 3.13E‐15 ‐0.361 3 14.0 Q2 Page 1 Dengjel et al. 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BioSyst., 2010, Supplementary Material (ESI) for Molecular BioSystems DOI: 10.1039/c003962d This journal is (c) The Royal Society of Chemistry, 2010 IPI00455473; MIA3 5.6 3.30E‐69 ‐0.360 2 15.0 Q2 IPI00032292; TIMP1 24.6 9.12E‐26 ‐0.321 4 17.2 Q2 IPI00871585; BID 11.1 8.30E‐51 ‐0.321 3 15.3 Q2 IPI00394994; C14orf49 4 4.51E‐22 ‐0.320 2 20.3 Q2 IPI00024775; RAB7L1 10.8 1.55E‐19 ‐0.320 2 35.1 Q2 IPI00016621; AP2A2 25 <1.0E‐304 ‐0.313 7 48.8 Q2 IPI00005573; NT5C 18.9 3.08E‐23 ‐0.305 2 15.6 Q2 IPI00783109; MTSS1L 7.2 3.32E‐10 ‐0.296 2 3.0 Q2 IPI00913924; LRRC15 25.9 7.68E‐125 ‐0.286 8 7.0 Q2 IPI00477611; COL5A1 4.9 7.86E‐32 ‐0.278 5 14.0 Q2 IPI00002606; SCIN 7.1 3.37E‐12 ‐0.278 3 2.5 Q2 IPI00329719; MYO1D 54.9 <1.0E‐304 ‐0.266 37 11.8 Q2 IPI00024642; CCDC47 15.7 2.45E‐34 ‐0.265 2 0.5 Q2 IPI00639812; MGST3 16.9 1.83E‐97 ‐0.262 2 1.9 Q2 IPI00103467; ALDH1B1 23.8 6.40E‐265 ‐0.262 3 6.2 Q2 IPI00304577; AP2A1 48.8 <1.0E‐304 ‐0.262 34 34.0 Q2 IPI00171412; SUMF2 22.5 6.80E‐82 ‐0.261 4 9.0 Q2 IPI00007675; DYNC1LI1 14.3 9.42E‐74 ‐0.260 3 21.1 Q2 IPI00643567 CAP1 18.2 <1.0E‐304 ‐0.260 3 15.3 Q2 IPI00640525; PPGB 19.1 1.54E‐91 ‐0.256 4 7.4 Q2 IPI00303602; AIDA 11.4 5.65E‐10 ‐0.252 2 18.1 Q2 IPI00900260; ARHGEF7 12 1.95E1.95E‐91 ‐00.252.252 2 18.218.2 Q2 IPI00247063; MME 54.7 <1.0E‐304 ‐0.248 33 8.9 Q2 IPI00018953; DPP4 41.9 <1.0E‐304 ‐0.247 28 16.6 Q2 IPI00152695; WDR82 17.3 1.06E‐41 ‐0.245 2 20.5 Q2 IPI00303195; SYNC 6.8 1.31E‐25 ‐0.244 2 37.0 Q2 IPI00291136 COL6A1 40.1 <1.0E‐304 ‐0.238 28 6.3 Q2 IPI00908768; HSPB6 43.9 1.67E‐76 ‐0.238 3 5.5 Q2 IPI00009896; EPHX1 28.6 5.26E‐56 ‐0.236 8 14.9 Q2 IPI00000230; DKFZp586K2222 48.9 3.25E‐272 ‐0.236 11 17.6 Q2 IPI00182728; VPS4B 16 1.67E‐47 ‐0.234 3 15.2 Q2 IPI00465428; VPS13C 4.6 7.09E‐49 ‐0.234 8 8.4 Q2 IPI00887461; HLA‐B 29.3 3.54E‐170 ‐0.232 6 7.1 Q2 Page 2 Dengjel et al. 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BioSyst., 2010, Supplementary Material (ESI) for Molecular BioSystems DOI: 10.1039/c003962d This journal is (c) The Royal Society of Chemistry, 2010 IPI00003766 ETHE1 36.2 2.02E‐67 ‐0.231 4 19.3 Q2 IPI00292894 TSR1 3.6 1.16E‐03 ‐0.230 2 40.6 Q2 IPI00295595; CERCAM 7.1 3.24E‐28 ‐0.229 2 1.8 Q2 IPI00028564; GBP1 23.1 9.18E‐48 ‐0.229 9 24.0 Q2 IPI00018352; UCHL1 53.8 4.30E‐202 ‐0.229 19 4.3 Q2 IPI00288947; GNAQ 19.2 1.05E‐82 ‐0.225 2 0.5 Q2 IPI00021057; SLC12A4 7.9 8.01E‐12 ‐0.225 5 26.9 Q2 IPI00095891; GNAS 8.5 3.95E‐32 ‐0.223 3 5.2 Q2 IPI00790064; NDUFB9 19 4.45E‐53 ‐0.219 2 23.0 Q2 IPI00796919; GLB1 22.5 3.73E‐190 ‐0.217 6 8.6 Q2 IPI00012119; DCN 21.4 1.22E‐40 ‐0.214 3 8.2 Q2 IPI00295741; CTSB 46.9 <1.0E‐304 ‐0.213 17 19.4 Q2 IPI00028565; GBP2 6.9 1.45E‐09 ‐0.210 2 3.5 Q2 IPI00296485 MAP1S 5.6 1.31E‐17 ‐0.208 2 21.0 Q2 IPI00014572 SPARC 26.1 9.58E‐69 ‐0.207 5 42.2 Q2 IPI00031479; PDIA5 14.1 2.50E‐18 ‐0.206 3 11.3 Q2 IPI00156689; VAT1 61.3 <1.0E‐304 ‐0.205 32 7.9 Q2 IPI00220278; MYL9 46.5 <1.0E‐304 ‐0.202 5 3.3 Q2 IPI00745313; AEBP1 9.3 2.77E‐63 ‐0.200 6 4.0 Q2 IPI00016373; RAB13 21.2 1.21E‐35 ‐0.200 2 1.9 Q2 IPI00014533; UBTF 8 6.16E‐19 ‐0.200 3 17.4 Q2 IPI00290279; ADK 27.127.1 6.67E6.67E‐75 ‐00.200.200 5 19.819.8 Q2 IPI00002824; CSRP2 61.7 7.58E‐69 ‐0.200 6 4.4 Q2 IPI00554521; FTH1 44.3 3.51E‐51 ‐0.198 7 40.0 Q2 IPI00029111; LCRMP 44 <1.0E‐304 ‐0.198 11 9.8 Q2 IPI00299066; LPXN 22 2.03E‐151 ‐0.193 3 0.5 Q2 IPI00009946; TOMM34 18.8 6.18E‐17 ‐0.192 3 18.7 Q2 IPI00797603; PRPSAP1 15.1 6.69E‐37 ‐0.192 3 21.6 Q2 IPI00011229; CTSD 48.3 <1.0E‐304 ‐0.192 33 15.3 Q2 IPI00022200; COL6A3 54.5 <1.0E‐304 ‐0.191 355 18.9 Q2 IPI00293088; GAA 24.5 <1.0E‐304 ‐0.190 4 22.2 Q2 IPI00009236; CAV1 50 6.46E‐153 ‐0.190 19 6.3 Q2 IPI00291238; FBLIM1 22.3 6.70E‐51 ‐0.190 3 10.5 Q2 Page 3 Dengjel et al. 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BioSyst., 2010, Supplementary Material (ESI) for Molecular BioSystems DOI: 10.1039/c003962d This journal is (c) The Royal Society of Chemistry, 2010 IPI00375631 ISG15 13.3 1.45E‐05 ‐0.187 2 33.3 Q2 IPI00058192; POFUT1 9.3 7.10E‐38 ‐0.186 3 11.4 Q2 IPI00873226; hTGP 1.3 2.86E‐03 ‐0.186 2 14.5 Q2 IPI00375676; FTL 35.6 1.27E‐122 ‐0.186 5 9.4 Q2 IPI00011932 HSPA12A 9.5 2.46E‐30 ‐0.184 2 1.2 Q2 IPI00022745; MVD 8.5 2.11E‐34 ‐0.183 2 23.4 Q2 IPI00018769; THBS2 10.4 1.34E‐122 ‐0.183 7 10.6 Q2 IPI00298111; SNX6 31.1 6.07E‐81 ‐0.182 6 15.4 Q2 IPI00328113; FBN1 2 1.00E‐21 ‐0.179 3 36.3 Q2 IPI00470529; GPNMB 5.8 9.65E‐109 ‐0.179 14 11.4 Q2 IPI00026314; GSN 51.3 <1.0E‐304 ‐0.178 42 9.2 Q2 IPI00166955; CNPY4 6.2 3.49E‐97 ‐0.177 2 2.7 Q2 IPI00871680; ARFGAP2 14 1.55E‐136 ‐0.177 2 18.9 Q2 IPI00332106; PBXIP1 21.9 1.86E‐146 ‐0.177 6 8.5 Q2 IPI00743696; COL4A1 4 1.82E‐08 ‐0.177 2 13.1 Q2 IPI00021264 CNN1 42.4 1.67E‐126 ‐0.177 4 3.9 Q2 IPI00856045; AHNAK2 41.1 <1.0E‐304 ‐0.177 107 15.0 Q2 IPI00023510; RAB5A 35.3 1.11E‐94 ‐0.177 8 14.5 Q2 IPI00056334; PRKCDBP 50.2 7.35E‐130 ‐0.177 9 9.6 Q2 IPI00025318; SH3BGRL 56.1 5.58E‐74 ‐0.176 5 7.9 Q2 IPI00296157; RETSAT 8.2 1.73E‐26 ‐0.176 2 8.8 Q2 IPI00884192; GPX4 33.833.8 9.09E9.09E‐63 ‐00.173.173 4 4.54.5 Q2 IPI00028122; PSIP1 8.7 9.10E‐63 ‐0.173 4 12.7 Q2 IPI00060627 CCDC124 25.1 1.83E‐09 ‐0.173 2 1.3 Q2 IPI00385495; LMF2 11.2 1.33E‐72 ‐0.172 8 20.1 Q2 IPI00100673; VPS24 20.3 2.34E‐07 ‐0.171 2 1.9 Q2 IPI00004312; STAT2 29.5 3.44E‐227 ‐0.171 22 23.9 Q2 IPI00168878 TOR1AIP2 9.8 6.53E‐23 ‐0.171 3 3.7 Q2 IPI00797038; PCK2 31.2 3.47E‐231 ‐0.170 9 9.5 Q2 IPI00018248; KDELR2 8 9.59E‐36 ‐0.170 6 12.2 Q2 IPI00329696; FAM82B 24.2 3.48E‐23 ‐0.170 4 20.4 Q2 IPI00007084 SLC25A13 23.1 6.33E‐230 ‐0.170 5 13.4 Q2 IPI00003128; P4HA2 45.6 <1.0E‐304 ‐0.169 4 2.1 Q2 Page 4 Dengjel et al.