Supplemental Table II. Identification of Non Ribosomal-Proteins Separated by NEpHGE/SDS-PAGE by use of Mass Spectrometry.

Non-ribosomal proteins separated by NEpHGE 2D gel systems and analyzed by PMF after trypsin digestion using MALDI-TOF, or tandem MS using triple Q-TOF with oMALDI or ESI as the ionization source. The protein number corresponds to the designation of the protein spot in Figure 2B. Mass values that matched a theoretical mass value of a particular peptide are shown in m/z. Peptides sequenced by ESI Q-TOF are indicated in bold. Only parental masses are shown in the table. Peptides identified by oMALDI are indicated in italics. Ribosomes were separated by sucrose gradient density centrifugation to obtain polysomes that were further fractionated by 1D SDS-PAGE. Seven gel sections were obtained and the proteins were digested with trypsin. The resulting peptides were separated by LC and analyzed by ESI MS/MS. Peptides that corresponded to proteasome subunits and the WD-domain repeat protein found in the polysome fraction are indicated in both italics and bold. Peptides that matched the product of a specific gene family member are indicated.

Non-Ribosomal Protein / pI / Molecular Mass / Sequence / Entry / Theoretical / Missed / Peptide Sequence / Specific to Gene
Number and Identification / Range / Range
(kDa) / Coverage
(%) / Mass (m/z) / Mass (m/z) / Cleavage / Family Member(s)
1
20S proteasome alpha subunit A / 5.7-6.0 / 27.3-27.4 / 39 / 801.469 / 801.458 / 0 / (R)SLVQQAR(N)
836.432 / 836.390 / 0 / (R)NEAAEFR(F) / At2g05840
1072.623 / 1072.600 / 0 / (K)ATEIEVGVVR(A)
1144.598 / 1144.604 / 0 / (R)LFQVEYAFK(A)
1156.608 / 1156.517 / 1 / (-)MSRGSGAGYDR(H)
1156.608 / 1156.612 / 0 / (R)HITIFSPEGR(L)
1484.755 / 1484.742 / 0 / (K)YLGLLATGMTADSR(S) + oxidation (M) / At2g05840
1642.783 / 1642.792 / 0 / (R)TEEIDEHLTAISER(D) / At2g05840
1670.916 / 1670.912 / 0 / (K)LLDQSSVSHLFPVTK(Y) / At2g05840
2
20S proteasome alpha subunit B / 5.5 / 25.7 / 47 / 1035.557 / 1035.559 / 1 / (R)KQAEQYLR(L)
1526.865 / 1526.879 / 1 / (K)KLPSILVDEASVQK(I)
1555.913 / 1555.921 / 1 / (R)LYKEPIPVTQLVR(E)
1850.853 / 1850.845 / 0 / (-)GDSQYSFSLTTFSPSGK(L)
1958.923 / 1958.929 / 0 / (K)GPQLYQVDPSGSYFSWK(A)
2122.187 / 2122.187 / 0 / (K)LVQIEHALTAVGSGQTSLGIK(A)
2217.106 / 2217.113 / 0 / (K)IQHLTPNIGVVYSGMGPDFR(V) / At1g17460
3
20S proteasome alpha subunit E / 4.5 / 25.9-26.0 / 43 / 825.461 / 825.458 / 0 / (R)TLVEHAR(V)
883.443 / 883.439 / 0 / (R)VETQNHR(F)
943.540 / 943.546 / 0 / (V)VLAVEK(R)
1063.529 / 1063.517 / 0 / (R)GVNTFSPEGR(L)
1070.630 / 1070.885 / 0 / (K)VTPNNVDIAK(V)
1399.788 / 1399.768 / 0 / (R)ITSPLLEPSSVEK(I)
1423.807 / 1423.784 / 0 / (R)LFQVEYAIEAIK(L)
1555.928 / 1555.870 / 1 / (K)RITSPLLEPSSVEK(I)
1729.982 / 1729.959 / 0 / (K)DLSLQEAETIAVSILK(Q) / At1g53850
1924.928 / 1924.889 / 0 / (K)AIGSGSEGADSSLQEQFNK(D)
2127.140 / 2127.124 / 0 / (K)VAPAYHLYTPQEVEAVIAR(L) / At1g53850
2143.131 / 2143.119 / 0 / (K)VAPAYHLYTPQEVEAVISR(L) / At3g14290
4
Vacuolar H+- ATPase chain E / 5.8-9.2 / 26.1-27.1 / 40 / 816.457 / 816.458 / 0 / (K)DLLNVSR(D) / AT4g11150
872.539 / 872.539 / 1 / (R)MKLPVIR(K) / AT4g11150
901.455 / 901.457 / 0 / (R)QIQQMVR(F)
908.561 / 908.561 / 0 / (K)IFLPPPPK(S) / AT4g11150
1054.660 / 1054.663 / 1 / (R)LKEPSVLLR(C)
1313.600 / 1313.616 / 0 / (K)IDYSMQLNASR(I)
1808.845 / 1808.838 / 1 / (-)MNDGDVSRQIQQMVR(F) / AT4g11150
1808.845 / 1808.855 / 0 / (K)ANEISVSAEEEFNIEK(L) / AT4g11150
1876.892 / 1876.909 / 0 / (K)SNDPHGLHCSGGVVLASR(D)
2225.099 / 2225.092 / 2 / (-)MNDGDVSRQIQQMVRFIR(Q) / AT4g11150
5
Vacuolar membrane H+-ATPase subunit G / 5.5-5.8 / 11.7-12.4 / 1122.500 / 1122.518 / (K)AQTEQDFQR(K)
1303.750 / 1306.613 / (K)LEETSGDSGANVK(R)
6
Chaperonin HSP60 / 5.7-6.4 / 60.5-62.1 / 12 / 847.428 / 847.406 / 0 / (K)APGFGENR(K)
932.449 / 932.505 / 0 / (R)VTDALNATK(A)
1204.600 / 1204.621 / (L)LEQDNPDLGY(D)
1524.781 / 1524.762 / 0 / (K)TLFNELEVVEGMK(L)
1661.800 / 1661.802 / (L)LEQDNPDLGY(D)
1927.078 / 1927.065 / 0 / (K)AAVEEGILPGGGVALLYAAR(E) / AT3g23990
2211.105 / 2211.250 / 1 / (K)LPTANFDQKIGVQIIQNALK(T) / At3g23990
7
Mitochondrial F0-ATPase synthase chain D / 5.1 / 19.6 / 1131.700 / 1131.582 / (K)EIADVQEISK(K) / At3g52300
8
Reversibly glycosylated polypeptide / 5.1-6.6 / 38.6-41.9 / 38 / 839.445 / 839.442 / 0 / (R)GYPFSLR(E)
989.535 / 989.542 / 0 / (K)ASNPFVNLK(K)
1037.508 / 1037.509 / 0 / (R)NLDFLEMR(R)
1117.552 / 1117.637 / 1 / (K)ASNPFVNLK(K)
1122.612 / 1122.627 / 0 / (K)AVNALEQHIK(N)
1184.581 / 1184.584 / 0 / (K)LSSLDPYFDK(L) / AT5g15650
1194.598 / 1194.605 / 0 / (K)LSPIDPYFDK(L) / AT3g02230
1283.711 / 1283.721 / 0 / (K)DELDIVIPTIR(N)
1620.764 / 1620.762 / 0 / (K)YIFTIDDDCFVAK(D)
1767.806 / 1767.834 / 0 / (K)IHVPEGYDYELYNR(N) / At5g15650
1775.750 / 1775.792 / 0 / (K)GTLFPMCGMNLAFDR(D)
1786.825 / 1786.865 / 0 / (K)TIAVPEGFDYELYNR(N) / At3g02230
1809.885 / 1809.892 / 2 / (K)ERNTRYVDAVMTNPK(G)
1901.019 / 1901.075 / 0 / (-)VEPANTVGLPVNPTPLLK(D) / At5g15650
1953.096 / 1953.117 / 2 / (-)VEPANTVGIPVNHIPLLK(D) / At3g02230
2139.996 / 2140.021 / 0 / (R)DLIGPAMYFGLMGDGQPIGR(Y) / At5g15650
2365.119 / 2365.133 / 0 / (K)NLLCPSSPFFFNTLYDPYR(E) / AT5g15650
2398.159 / 2398.273 / 2 / (K)LTKEAVTVQQCYMELSKLVK(E) / At3g02230
8
Reversibly glycosylated polypeptide / 5.1-6.6 / 38.6-41.9 / 33 / 989.536 / 989.542 / 0 / (K)ASNPFVNLK(K)
1178.635 / 1178.621 / 0 / (K)TGLPYIYHSK(A)
1194.589 / 1194.605 / 0 / (K)LSPIDPYFDK(L) / AT3g02230
1261.659 / 1261.644 / 2 / (R)CFGYMVSKKK(Y)
1283.725 / 1283.721 / 0 / (K)DELDIVIPTIR(N)
1620.792 / 1620.762 / 0 / (K)YIFTIDDDCFVAK(D)
1775.863 / 1775.792 / 0 / (K)GTLFPMCGMNLAFDR(E)
1786.910 / 1786.865 / 0 / (K)TIAVPEGFDYELYNR(N) / At3g02230
2300.266 / 2300.127 / 0 / (K)LADAMVTWIEAWDELNPPTK(A) / At3g02230
2399.303 / 2399.163 / 1 / (K)TIAVPEGFDYELYNRNDINR(I) / At3g02230
9
Glutamine synthase / 38.6-47.4 / 5.1-6.4 / 15 / 1345.601 / 1345.614 / 0 / (K)EHIAAYGEGNER(R)
1427.675 / 1427.684 / 1 / (K)SMREEGGYEIIK(K)
1449.784 / 1449.795 / 0 / (R)TLPGPVTDPSQLPK(W)
1610.752 / 1610.768 / 1 / (R)HKEHIAAYGEGNER(R)
1829.821 / 1829.857 / 0 / (K)IIAEYIWVGGSGMDMR(S)
1876.000 / 1875.958 / (-)SDLINLNL(-)
9
Glutamine synthase 1 (cytosolic) / 38.6-47.4 / 5.1-6.4 / 36 / 801.495 / 801.470 / 1 / (R)GASVRVGR(D)
960.476 / 960.479 / 0 / (R)DIVDAHYK(A)
1338.709 / 1338.738 / 1 / (K)ARTLPGPVTDPSK(L)
1345.616 / 1345.614 / 0 / (K)EHIAAYGEGNER(R)
1348.650 / 1348.690 / 1 / (K)TMRNDGGLEVIK(K)
1460.773 / 1460.790 / 2 / (K)TMRNDGGLEVIKK(A) / At3g17820
1793.872 / 1793.926 / 0 / (K)IIAEYIWIGGSGMDIR(S)
1815.916 / 1815.970 / 0 / (-)SLLSDLVNLNLTDATGK(I) / At3g17820
1816.000 / 1815.970 / (-)SDLVNLNL(-)
2217.032 / 2217.105 / 1 / (R)LTGKHETADINTFSWGVANR(G)
2366.125 / 2366.174 / 0 / (R)RPASNMDPYVVTSMIAETTILG(-) / At3g17820
2398.186 / 2398.163 / 0 / (R)RPASNMDPYVVTSMIAETTILG(-) / At3g17820
10
WD-domain repeat containing protein (RACK1 ortholog) / 6.7-7.6 / 35.7-35.8 / 34 / 890.447 / 890.462 / 0 / (K)IWDLESK(S)
935.438 / 935.441 / 0 / (R)DWVSCVR(F) / At1g18080
1134.559 / 1134.562 / 0 / (K)LWNTLGECK(Y)
1188.626 / 1188.638 / 0 / (R)LWDLAAGVSTR(R) / At1g18080
1248.605 / 1248.622 / 0 / (R)LWDLATGESTR(R) / At1g48630
1323.635 / 1323.655 / 0 / (K)DVLSVAFSLDNR(Q)
1335.675 / 1335.667 / 1 / (K)MWNLSNCKLR(S)
1335.675 / 1335.691 / 0 / (K)DVLSVAFSLDNR(Q) / At1g18080
1414.720 / 1414.758 / 0 / (K)DGVVLLWDLAEGK(K) / At1g18080
1462.691 / 1462.715 / 0 / (R)YWLCAATEHGIK(I) / At1g18080