Table 1A (supplemental data). Summary of nano-LC-ESI-MS/MS data from the CN-PAGE gel (Figure 2A) gel of stroma of A. thaliana chloroplasts. Complementary MALDI-TOF MS data are not listed. The spots were picked in the Clp complex from low to high molecular mass.Z is the charge state of the measured precursor ion.MH+ is thecalculated mass of the protonated precursor ion. Only sequence tags matching to Clp proteins are listed.
Precursor Ion / Z / MH+ / sequence / IDspot 9 / 508.7 / 2 / 1015.39 / AIAWAIDEK / clpS1
650.70 / 2 / 1299.39 / SM(ox)NEDVDLSFK / clpS1
642.70 / 2 / 1283.39 / SMNEDVDLSFK / clpS1
928.9 / 2 / 1855.8 / ...VLLVPLAQPENG… / clpS1
488.2 / 2 / 974.39 / DETLSLLGK / clpS1
563.7 / 2 / 1125.39 / SFAM(ox)GELEAR / clp S2
594.3 / 2 / 1186.59 / ALDSALDQNLK / clpS2
604.3 / 2 / 1206.59 / ILATLGFTDEK / clpS2
678.30 / 2 / 1354.59 / MYAAFTGQPLEK / clpP6
834.40 / 2 / 1666.79 / IIFIGQPINAQVAQR / clpP6
848.30 / 2 / 1694.59 / SPGEGDTSWVDIYNR / clpP1
695.80 / 2 / 1389.59 / PIWVISEDM(ox)ER / clpP1
spot 10 / 789.3 / 2 / 1576.59 / EYGLIDGVIM(ox)NPLK / clpP5
939.90 / 2 / 1877.79 / ANLNGYLAYHTGQSLEK / clpP5
661.80 / 2 / 1321.59 / 168-QGPPPM(ox)VQER / clpP5
852.40 / 2 / 1702.79 / INQDTDRDFFMSAK / clpP5
678.30 / 2 / 1354.59 / MYAAFTGQPLEK / clpP6
834.40 / 2 / 1666.79 / IIFIGQPINAQVAQR / clpP6
594.3 / 2 / 1186.59 / ALDSALDQNLK / clpS2
604.3 / 2 / 1206.59 / ILATLGFTDEK / clpS2
887.90 / 2 / 1773.79 / SKELESFASESGFLDE / clpS2
615.80 / 2 / 1229.59 / VRDETLSLLGK / clpS1
746.71 / 3 / 2237.09 / SDM(ox)YFFSPEHPPLTEPAQK / clpS1
848.30 / 2 / 1694.59 / SPGEGDTSWVDIYNR / clpP1
732.71 / 3 / 2195.09 / STVLNVPLAQPENGSSDKIPK / clpP1
spot 11 / 765.3 / 2 / 1528.59 / FQSIISQLFQYR / clpP5
626.91 / 3 / 1877.69 / ANLNGYLAYHTGQSLEK / clpP5
781.3 / 2 / 1560.59 / EYGLIDGVIMNPLK / clpP5
789.3 / 2 / 1576.59 / EYGLIDGVIM(ox)NPLK / clpP5
939.9 / 2 / 1877.79 / ANLNGYLAYHTGQSLEK / clpP5
661.80 / 2 / 1321.59 / 168-QGPPPM(ox)VQER / clpP5
626.91 / 3 / 1877.69 / ANLNGYLAYHTGQSLEK / clpP5
563.21 / 3 / 1686.59 / INQDTDRDFFMSAK / clpP5
789.3 / 2 / 1576.59 / EYGLIDGVIM(ox)NPLK / clpP5
765.3 / 2 / 1528.59 / FQSIISQLFQYR / clpP5
661.80 / 2 / 1321.59 / 168-QGPPPM(ox)VQER / clpP5
789.3 / 2 / 1576.59 / EYGLIDGVIM(ox)NPLK / clpP5
626.91 / 3 / 1877.69 / ANLNGYLAYHTGQSLEK / clpP5
833.90 / 2 / 1665.79 / IIFIGQPINAQVAQR / clpP6
spot 12 / 527.80 / 2 / 1053.59 / IALQSPAGAAR / clpR2
556.80 / 2 / 1111.59 / DYLFNELAK / clpR2
806.40 / 2 / 1610.79 / FNAEEAIEYGLIDK / clpR2
spot 13 / 667.80 / 2 / 1333.59 / FQGQATDVEIAR / clp R4
866.40 / 2 / 1730.79 / YFSPTEAVEYGIIDK / clp R4
619.61 / 3 / 1855.79 / GSAHEQPPPDLASYLFK / clp R4
spot 14 / 425.6 / 2 / 849.3 / SFEQVLK / clpP4
726.38 / 2 / 1450.75 / FLTPEIPDDEIY / clpP4
696.8 / 2 / 1391.68 / NNVTSIIAGCTSR / clpP4
638.80 / 2 / 1275.59 / GAESDVM(ox)GLLLR / clpP4
764.71 / 3 / 2291.09 / IMIHQPLGGASGQAIDVEIQAK / clpP4
667.80 / 2 / 1333.59 / FQGQATDVEIAR / clpR4
866.4 / 2 / 1730.79 / YFSPTEAVEYGIID / clpR4
785.4 / 2 / 1568.79 / MEVAAATATSFTTLR / clpR4
582.30 / 2 / 1162.59 / SALPSSTIM(ox)IK / ClpR4
spot 15 / 515.30 / 2 / 1028.59 / DILVELLSK / clpR3
649.01 / 3 / 1943.99 / IIADVVPSEEFDKNAGIK / clpR3
731.30 / 2 / 1460.59 / IIADVVPSEEFDK / clpR3
814.40 / 2 / 1626.79 / EPIYIYINSTGTTR / clpR3
731.37 / 2 / 1460.73 / IIADVVPSEEFDK / clpR3
779.40 / 2 / 1556.79 / VPSSGLMPASDVLIR / clpR3
940.71 / 3 / 2819.09 / EYGLIDAVIDDGKPGLIAPIGDGTPPPK / clpP3
617.29 / 2 / 1232.57 / DNFLNPWEAK / clpP3
423.70 / 2 / 845.39 / VWDLWK / clpP3
723.31 / 3 / 2889.19 / ITGKPESEIESDTDRDNFLNPWEAK / clpP3
897.90 / 2 / 1793.79 / LPSFEELDTTNM(ox)LLR / clpP3
617.30 / 2 / 1232.59 / DNFLNPWEAK / clpP3
820.40 / 2 / 1638.79 / YLQAQAAIDYGIADK / clpR1
892.9 / 2 / 1783.79 / ELDANTEYYIELLAK / clpR1
710.3 / 3 / 2127.07 / ELDANTEYYIELLAKGTGK / clpR1
Table 1B (Supplemental data). Summary of nano-LC-ESI-MS/MS data from the CN-PAGE gel (Figure 2B) of peripheral thylakoid proteins of A. thaliana chloroplasts. Complementary MALDI-TOF MS data are not listed. The spots were picked in the Clp complex from low to high molecular mass.Z is the charge state of the measured precursor ion.Only sequence tags matching to Clp proteins are listed.
sample / Precursor ion / Z / sequence / identitySpot 16 / 848.3 / 2 / SPGEGDTSWVDIYNR / ClpP1
1027.5 / 3 / VMIHQPASSFYEAQTGEFILEAEELLK / ClpP1
1053.8 / 3 / LFFLGQEVDTEISNQLISLmIYLSIEK / ClpP1
710 / 3 / SPGEGDTSWVDIYNRLYR / ClpP1
554.3 / 3 / TGKPIWVISEDMER / ClpP1
672.7 / 3 / VGTVAFGVAASQGALLLAGGEK / ClpP6
686.3 / 2 / MYAAFTGQPLEK / ClpP6
751.4 / 2 / VISQLVTLASIDDK / ClpP6
690.3 / 4 / HIRPDVSTVCVGLAASMGAFLLSAGTK / ClpP5
627 / 3 / ANLNGYLAYHTGQSLEK / ClpP5
959.7 / 3 / CGGAVDDDMANIIVAQLLYLDAVDPTK / ClpP5
789.4 / 2 / EYGLIDGVImNPLK / ClpP5
Spot 17 / 732.3 / 3 / SDVDGELTTAYLLLGVWSQK / ClpS1
780 / 3 / YPSTGTEAILMGILVEGTSTVAK / ClpS1
476.9 / 3 / SmNEDVDLSFKK / ClpS1
650.7 / 2 / SmNEDVDLSFK / ClpS1
746.3 / 3 / SDmYFFSPEHPPLTEPAQK / ClpS1
546.7 / 2 / SLAmGELEAR / ClpS1
508.7 / 2 / AIAWAIDEK / ClpS1
488.2 / 2 / DETLSLLGK / ClpS1
771.8 / 4 / ImIHQPLGGAQGGQTDIDIQANEmLHHK / ClpP5
690.3 / 4 / HIRPDVSTVCVGLAASMGAFLLSAGTK / ClpP5
568.6 / 3 / INQDTDRDFFmSAK / ClpP5
789.4 / 2 / EYGLIDGVImNPLK / ClpP5
860.7 / 3 / DIVmYVNSPGGSVTAGmAIFDTmR / ClpP5
959.4 / 3 / CGGAVDDDMANIIVAQLLYLDAVDPTK / ClpP5
672.7 / 3 / VGTVAFGVAASQGALLLAGGEK / ClpP6
834.4 / 2 / IIFIGQPINAQVAQR / ClpP6
751.4 / 2 / VISQLVTLASIDDK / ClpP6
820.4 / 3 / YPNTGTEALLmGILIEGTSFTSK / ClpS2
756.3 / 3 / ADmYFFSPEHPPLTEDAQR / ClpS2
604.3 / 2 / ILATLGFTDEK / ClpS2
594.3 / 2 / ALDSALDQNLK / ClpS2
848.3 / 2 / SPGEGDTSWVDIYNR / ClpP1
1032.8 / 3 / VmIHQPASSFYEAQTGEFILEAEELLK / ClpP1
694.3 / 4 / HIRPDVSTVCVGLAASmGAFLLSAGTK / ClpP5
626.9 / 3 / ANLNGYLAYHTGQSLEK / ClpP5
959.4 / 3 / CGGAVDDDMANIIVAQLLYLDAVDPTK / ClpP5
789.4 / 2 / EYGLIDGVImNPLK / ClpP5
860.7 / 3 / DIVmYVNSPGGSVTAGmAIFDTmR / ClpP5
568.6 / 3 / INQDTDRDFFmSAK / ClpP5
Spot 18 / 834.4 / 2 / IIFIGQPINAQVAQR / ClpP6
751.4 / 2 / VISQLVTLASIDDK / ClpP6
672.7 / 3 / VGTVAFGVAASQGALLLAGGEK / ClpP6
834.1 / 3 / GNPPVmPSVmTPGGPLDLSSVLFR / ClpP6
514.7 / 2 / QVNEAIEAR / ClpP6
1098 / 2 / SDVDGELTTAYLLLGVWSQK / ClpS1
746.3 / 3 / SDmYFFSPEHPPLTEPAQK / ClpS1
785.4 / 3 / YPSTGTEAILmGILVEGTSTVAK / ClpS1
508.8 / 2 / AIAWAIDEK / ClpS1
848.3 / 2 / SPGEGDTSWVDIYNR / ClpP1
559.6 / 3 / TGKPIWVISEDmER / ClpP1
1032.8 / 3 / VmIHQPASSFYEAQTGEFILEAEELLK / ClpP1
604.3 / 2 / ILATLGFTDEK / ClpS2
686 / 3 / AFGIIDEVIDERPLELVK / ClpP2
Spot 19 / 1163.8 / 3 / VIFIGQNIDEEFSNQILATmLYLDTLDDSR / ClpR2
815.7 / 3 / SPVGTHCVGLAYNLAGFLLAAGEK / ClpR2
589.9 / 3 / RFNAEEAIEYGLIDK / ClpR2
806.3 / 2 / FNAEEAIEYGLIDK / ClpR2
527.8 / 2 / IALQSPAGAAR / ClpR2
855.7 / 3 / IYmYLNGPGGDLTPSLAIYDTmK / ClpR2
461.2 / 3 / IRDYLFNELAK / ClpR2
594.7 / 2 / GQADDIQNEAK / ClpR2
619.6 / 3 / GSAHEQPPPDLASYLFK / ClpR4
582.2 / 2 / SPEQIEADmK / ClpR4
582.3 / 2 / SALPSSTImIK / ClpR4
626.9 / 3 / ANLNGYLAYHTGQSLEK / ClpP5
spot 20 / 815.7 / 3 / SPVGTHCVGLAYNLAGFLLAAGEK / ClpR2
1163.9 / 3 / VIFIGQNIDEEFSNQILATmLYLDTLDDSR / ClpR2
806.4 / 2 / FNAEEAIEYGLIDK / ClpR2
461.2 / 3 / IRDYLFNELAK / ClpR2
855.7 / 3 / IYmYLNGPGGDLTPSLAIYDTmK / ClpR2
556.7 / 2 / DYLFNELAK / ClpR2
594.8 / 2 / GQADDIQNEAK / ClpR2
527.8 / 2 / IALQSPAGAAR / ClpR2
582.3 / 2 / SALPSSTImIK / ClpR4
619.6 / 3 / GSAHEQPPPDLASYLFK / ClpR4
582.2 / 2 / SPEQIEADmK / ClpR4
667.8 / 2 / FQGQATDVEIAR / ClpR4
866.4 / 2 / YFSPTEAVEYGIIDK / ClpR4
734.4 / 3 / ADVSTIALGIAASTASIILGAGTK / ClpP4
spot 21 / 1101.1 / 2 / ADVSTIALGIAASTASIILGAGTK / ClpP4
764.7 / 3 / ImIHQPLGGASGQAIDVEIQAK / ClpP4
696.8 / 2 / NNVTSIIAGCTSR / ClpP4
856.4 / 3 / LFINSPGGSLSATmAIYDVVQLVR / ClpP4
537.5 / 4 / EVmHNKNNVTSIIAGCTSR / ClpP4
1130.2 / 3 / YmSPIEAVEYGLIDGVIDGDSIIPLEPVPDR / ClpP4
638.8 / 2 / GAESDVmGLLLR / ClpP4
490.2 / 3 / VNYEEISKDPmK / ClpP4
937.5 / 3 / IVFLGSSIDDFVADAImSQLLLLDAK / ClpP4
450.6 / 3 / SFEQVLKDIDR / ClpP4
515.9 / 3 / GAESDVMGLLLRER / ClpP4
582.2 / 2 / SPEQIEADmK / ClpR4
667.8 / 2 / FQGQATDVEIAR / ClpR4
619.6 / 3 / GSAHEQPPPDLASYLFK / ClpR4
559.6 / 3 / ITGKPESEIESDTDR / ClpP3
442.2 / 3 / VmIHQPLGTAGGK / ClpP3
897.9 / 2 / LPSFEELDTTNmLLR / ClpP3
527.8 / 2 / IALQSPAGAAR / ClpR2
Spot 22 / 734.4 / 3 / ADVSTIALGIAASTASIILGAGTK / ClpP4
696.8 / 2 / NNVTSIIAGCTSR / ClpP4
764.7 / 3 / ImIHQPLGGASGQAIDVEIQAK / ClpP4
638.8 / 2 / GAESDVmGLLLR / ClpP4
937.5 / 3 / IVFLGSSIDDFVADAImSQLLLLDAK / ClpP4
856.4 / 3 / LFINSPGGSLSATmAIYDVVQLVR / ClpP4
734.4 / 3 / ADVSTIALGIAASTASIILGAGTK / ClpP4
1130.3 / 3 / YMSPIEAVEYGLIDGVIDGDSIIPLEPVPDR+OX / ClpP4
800.1 / 3 / AmIQQPRVPSSGLmPASDVLIR / ClpR3
649 / 3 / IIADVVPSEEFDKNAGIK / ClpR3
940.2 / 3 / EYGLIDAVIDDGKPGLIAPIGDGTPPPK / ClpP3
613.8 / 2 / IADSQDSSFEK / ClpR1
Table 2C (Supplemental data) Summary of nano-LC-ESI-MS/MS data from the CN-PAGE gel (Figure 2C) gel of stromal proteins of A. thaliana chloroplasts. Complementary MALDI-TOF MS data are not listed. The spots (1 and 2) were picked in the ClpC complex indicated in Figure 2C.Z is the charge state of the measured precursor ion.Only sequence tags matching to Clp proteins are listed.
sample / Precursor Ion / Z / sequences / Identityspot 1 / 458.75 / 2 / AEVSAIQAK / ClpC1
486.76 / 2 / IIGQDEAVK / ClpC1
515.28 / 2 / TAIAEGLAQR / ClpC1 and ClpC2
526.24 / 2 / LLEDSMAEK+Ox / ClpC1 and ClpC2
558.81 / 2 / EIELQVTER / ClpC1 and ClpC2
580.31 / 2 / AIDLIDEAGSR / ClpC1 and ClpC2
588.31 / 2 / VIMLAQEEAR+OX / ClpC1
435.90 / 3 / LRHAQVPEEAR / ClpC1
658.31 / 2 / IASGDVPETIEGK / ClpC1 and ClpC2
677.84 / 2 / NNPCLIGEPGVGK / ClpC1 and ClpC2
699.38 / 2 / VLENLGADPSNIR / ClpC1 and ClpC2
481.93 / 3 / IASGDVPETIEGKK / ClpC1
496.60 / 3 / AIKVIMLAQEEAR+Ox / ClpC1
756.87 / 2 / MPTLEEYGTNLTK+Ox / ClpC1 and ClpC2
519.62 / 3 / EIELRAEVSAIQAK / ClpC1
528.60 / 3 / TKNNPCLIGEPGVGK / ClpC1 and ClpC2
618.62 / 3 / GELQCIGATTLDEYRK / ClpC1 and ClpC2
650.33 / 3 / VVDEGYNPSYGARPLRR / ClpC1
509.04 / 4 / QLGHNYIGSEHLLLGLLR / ClpC1 and ClpC2
678.39 / 3 / QLGHNYIGSEHLLLGLLR / ClpC1 and ClpC2
727.73 / 3 / FQPVKVPEPTVDETIQILK / ClpC1
589.83 / 4 / VGLKNPNRPIASFIFSGPTGVGK / ClpC1 and ClpC2
789.08 / 3 / NNPCLIGEPGVGKTAIAEGLAQR / ClpC1 and ClpC2
spot 2 / 457.78 / EIADILLK / ClpC1
458.75 / AEVSAIQAK / ClpC1
459.76 / SLVTEELK / ClpC1 and ClpC2
486.76 / IIGQDEAVK / ClpC1
511.77 / LDEMIVFR / ClpC1 and ClpC2
515.28 / TAIAEGLAQR / ClpC1 and ClpC2
518.76 / HAQVPEEAR / ClpC1
519.76 / LDEMIVFR+Ox / ClpC1 and ClpC2
526.24 / LLEDSMAEK+Ox / ClpC1 and ClpC2
558.81 / EIELQVTER / ClpC1 and ClpC2
579.82 / VLELSLEEAR / ClpC1 and ClpC2
580.31 / AIDLIDEAGSR / ClpC1 and ClpC2
587.25 / LDMSEFMER+ Ox / ClpC1 and ClpC2
588.31 / VIMLAQEEAR+OX / ClpC1 and ClpC2
595.25 / LDMSEFMER +2Ox / ClpC1 and ClpC2
403.22 / HIEKDPALER / ClpC1 and ClpC2
607.80 / IGFDLDYDEK / ClpC1 and ClpC2
435.90 / LRHAQVPEEAR / ClpC1 and ClpC2
658.31 / IASGDVPETIEGK / ClpC1 and ClpC2
677.84 / NNPCLIGEPGVGK / ClpC1 and ClpC2
461.59 / LAEEGKLDPVVGR / ClpC1 and ClpC2
699.38 / VLENLGADPSNIR / ClpC1 and ClpC2
715.92 / VITLDMGLLVAGTK / ClpC1 and ClpC2
481.93 / IASGDVPETIEGKK / ClpC1
482.94 / VITLDMGLLVAGTK+Ox / ClpC1 and ClpC2
738.89 / GSGFVAVEIPFTPR / ClpC1 and ClpC2
527.95 / VPEPTVDETIQILK / ClpC1 and ClpC2
791.44 / VPEPTVDETIQILK / ClpC1 and ClpC2
536.95 / RPYTVVLFDEIEK / ClpC1 and ClpC2
496.60 / AIKVIMLAQEEAR+Ox / ClpC1
756.87 / MPTLEEYGTNLTK+Ox / ClpC1 and ClpC2
519.62 / EIELRAEVSAIQAK / ClpC1
528.60 / TKNNPCLIGEPGVGK / ClpC1
903.52 / NTLLIMTSNVGSSVIEK / ClpC1 and ClpC2
607.99 / NTLLIMTSNVGSSVIEK +Ox / ClpC1 and ClpC2
618.62 / GELQCIGATTLDEYRK / ClpC1 and ClpC2
646.30 / IGFDLDYDEKDSSYNR / ClpC1 and ClpC2
653.68 / NPNRPIASFIFSGPTGVGK / ClpC1 and ClpC2
656.30 / MVGENNEVTANVGGGSSSNK+Ox / ClpC1
983.96 / MVGENNEVTANVGGGSSSNK+Ox / ClpC1
673.33 / AHPDVFNMMLQILEDGR+2 Ox / ClpC1 and ClpC2
509.04 / QLGHNYIGSEHLLLGLLR / ClpC1 and ClpC2
755.40 / LIGSPPGYVGYTEGGQLTEAVR / ClpC1 and ClpC2
765.04 / YTDESLVAAAQLSYQYISDR / ClpC1
1