Supplementary Table2: Protein Identification by LC-MS/MS, Respecting to Results of BN-PAGE

Supplementary Table 2: Protein identification by LC-MS/MS, with respecti to results of BN-PAGE separation presented in Table 1 and Figs. 5 and 6. Only the results of bands 5 to 8 are presented. Database: uniref100.fasta, 5888655 entries.

Protein band / protein name / gene / Peptide sequence / accession number / Organism / MH+
a / Z
b / P (pep)
c / XCorr
d
5 / ATP synthase subunit alpha / atpA / R.HTLIIYDDLSK.Q
K.NVGIVLMGDGLMIQEGSFVK.A
R.IIGLGEIMSGELVEFAEGTR.G
R.VINALAKPIDGRGEIVASESR.L
K.TFTEQAETLLK.E
K.QSQSNPLPVEEQVATIYTGTR.G
K.TFTEQAETLLKEAIQEQLER.F
R.RSVYEPLQTGLIAIDSMIPIGR.G
R.QGIPLITDRFDSLEQLDEFSR.S
R.IAQIPVSEAYLGR.V
R.LLESPAPGIISR.R
/ A1EA05
P05022
Q85FN4
A1EA25
Q3V549
Q19VA5
/ Agrostis stolonifera
Zea mays
Adiantum capillus-veneris
Agrostis stolonifera
Acorus calamus
Chlorokybus atmophyticus
/ 1317.70
2107.09
2121.08
2195.21
1280.67
2318.16
2377.22
2429.32
2479.24
1416.78
1252.72
/ 2
2
2
2
2
2
2
2
2
2
2
/ 2.37E-06
2.33E-14
9.33E-14
1.20E-07
1.72E-05
7.55E-13
2.47E-10
9.04E-08
4.39E-07
2.80E-08
6.19E-06
/ 0.07
6.07
5.67
5.30
2.77
5.19
5.36
5.67
3.13
3.65
3.63
plastoquinol-plastocyanin reductase - cytochrome f / petA / K.KGGLNVGAVIILPEGFELAPPDR.L
K.YSEIVFPILSPDPATK.K
-.SHPISAQQGYENPR.-
R.QVIDIIPPGPELLVSEGESIK.L
/ A7M973
A1EA21
Q2WGH0
Q6L387
/ Cuscuta reflexa
Agrostis stolonifera
Selaginella uncinata
Saccharum hybrid
/ 2362.31
1776.94
1583.75
2233.23
/ 2
2
2
2
/ 3.01E-12
3.27E-07
8.46E-04
3.39E-11
/ 6.32
5.07
3.12
3.03
PSII 47 kDa protein / psbB / R.RVSDGLAENLSLSEAWSK.I
R.MPTFFETFPVVLVDEEGIVR.A
R.AQLGEIFEXDRATXK.X
K.IPEKLAFYDYIGNNPAK.G
R.DVFAGIDPDLDAQVEFGTFQK.V
R.YQWDQGYFQKEIYR.R
K.YSVEQVGVTVEFYGGELDGVSYSDPATVKK.Y
R.AGAM*DNGDGIAVGWLGHPVFR.D
R.QGMFVLPFMTR.I
/ P05641
Q85AI7
Q8M9R9
Q85FJ7
P10900
A6YAG7
Q4FFM9
Q3ZPR5
Q06J24
/ Zea mays
Anthoceros formosae
Enkianthus chinensis
Adiantum capillus-veneris
Hordeum vulgare
Peridiscus lucidus
Ranunculus macranthus
Cleistes sp. Chase O-430
Bigelowiella natans
/ 1961.99
2325.18
1703.93
1953.01
2312.10
1923.90
3223.56
2156.03
1326.66
/ 2
2
2
2
2
2
3
2
2
/ 3.33E-10
1.87E-08
7.49E-08
7.92E-11
7.77E-15
4.10E-09
8.09E-11
1.12E-11
2.84E-05
/ 5.38
4.99
4.57
6.02
5.67
3.59
4.69
4.48
2.52
Photosystem II D2 protein / psbD / R.AWMAAQDQPHENLIFPEEVLPR.G
R.VTKEENDLFDIMDDWLR.R
R.AAEDPEFETFYTK.N
R.AYDFVSQELR.A
/ P69685
Q6ENJ1
Q85FM2
P28253
/ Antirrhinum majus
Oryza nivara
Adiantum capillus-veneris
Galdieria sulphuraria
/ 2591.27
2139.00
1547.69
1227.60
/ 2
2
2
2
/ 1.53E-11
2.55E-10
3.89E-09
1.02E-04
/ 6.17
5.73
4.33
3.78
ATP synthase subunit beta / atpB / R.AVAMSATEGLMR.G
R.IFNVLGEPIDNLGPVDTSATFPIHR.S
R.GMEVIDTGTPISVPVGGATLGR.I
-.TVXIMELINNIAK.-
K.AHGGVSVFGGVGER.T
R.FVQAGSEVSALLGR.M
R.DTADQQINVTCEVQQLLGNNR.V
R.DVNKQDVLXFIDNIFR.F
-.MPSAVGYQPTLSTEMGSXQER.-
R.TREGNDLYMEMKESGVINEK.N
K.GXYPAVDPLDSTSTMLQPR.I
R.IDKIIGPVLDITFPPGK.L
K.ALDAQIASLSDEIVKK.V
-.YKELQDIISVLGLDELSEEDRLTVAR.-
R.VGXTALTMAEYFR.D
-.FLSQPFFVAEVFTSSPGKYVGLAETIR.-
-.SAPAFIELDTK.-
/ P00827
Q7H8L7
Q95FP0
Q3V527
Q9MTT8
Q8MFV8
Q95FV3
Q7HDI4
Q9TLL7
Q008G3
A2XF65
O98411
Q9MRF4
A0ZQA8
P62626
/ Zea mays
Evolvulus nuttallianus
Mouriri cyphocarpa
Acorus calamus
Xanthophyllum sp. ‘Coode 7760 K’
Juniperus communis
Caryocar glabrum
Acrocomia aculeata
Glaucidium palmatum
Phyllostachys edulis
Oryza sativa subsp. Indica
Helianthemum grandiflorum
Heisteria parvifolia
Oldfieldia dactylophylla
Aegilops columnaris
/ 1236.60
2722.41
2127.11
1471.85
1328.67
1433.77
2416.15
1949.04
2282.07
2343.09
2061.03
1823.06
1700.94
3004.58
1471.76
2990.56
1191.62
/ 2
2
2
2
2
2
2
2
2
3
2
2
2
3
2
3
2
/ 1.91E-06
3.69E-11
3.83E-08
7.32E-06
3.02E-08
2.73E-06
1.71E-09
5.47E-09
6.54E-10
1.61E-09
1.62E-11
2.39E-07
1.20E-08
2.32E-07
2.18E-07
1.04E-04
1.96E-05
/ 3.42
4.47
5.39
4.21
4.21
4.89
5.28
6.00
5.76
5.65
5.49
5.38
5.08
4.73
4.38
3.13
2.69
Photosystem II 44 kDa protein / psbC / K.GIDRDLEPVLYM*TPLN.-
-.APWXEPXRGPNGLDLSR.-
R.SGEYM*THAPLGSLNSVGGVATEINAVNYVSPR.S
K.ITNLTLSPGVIFGYLLK.S
R.XGANVGSAQGPTGLGK.Y
R.SPTGEVIFGGETMR.F
/ Q6ENJ0
Q8HSZ9
P48187
Q67GZ0
P56778
/ Oryza nivara
Gunnera chilensis
Zea mays
Blandfordia punicea
A. thaliana
/ 1861.93
1891.01
3306.60
1849.08
1426.76
1480.71
/ 2
2
3
2
2
2
/ 1.26E-08
4.44E-07
4.82E-06
5.24E-05
1.84E-06
5.38E-08
/ 4.12
3.52
5.07
5.08
4.55
4.48
Cytochrome b6 / petB / K.VYDWFEERLEIQAIADDVTTK.Y
K.IVTGVPEAIPVIGSPLVEILR.G
/ B0C0E8
Q6YXN2
/ Acaryochloris marina (strain MBIC 11017)
Physcomitrella patens
/ 2541.25
2172.30
/ 2
2
/ 1.53E-09
3.06E-10
/ 5.02
3.68
ATP synthase subunit gamma / atpC / R.ALQESIASELAAR.M
R.SDPIIQTLLPMSPK.G
/ A9RY84
P0C1M0
/ Physcomitrella patens subsp. Patens
Zea mays
/ 1358.72
1539.84
/ 2
2
/ 7.20E-07
2.08E-05
/ 4.49
4.33
Photosystem Q(B) protein / psbA / -.VINTWADLLNR.-
R.ANLGMEVMHER.N
/ Q6SL63
P46242
/ uncultured cyanophage
Anabaena sp. (strain PCC 7120)
/ 1314.71
1286.59
/ 2
2
/ 1.77E-04
8.07E-05
/ 3.86
3.10
6 / PSII 47 kDa protein / psbB / K.LAFYDYIGNNPAK.G
R.RVSDGLAENLSLSEAWSK.I
R.YQWDQGYFQQEIYR.R
R.AGSMDNGDGIAVGWLGHPVFR.D
R.DVFAGIDPDLDAQVEFGTFQK.V
R.RAQLGEIFEXDR.A
/ P05641
Q8M9R9
/ Zea mays
Enkianthus chinensis
/ 1485.73
1961.99
1923.86
2172.02
2312.10
1446.76
/ 2
2
2
3
2
2
/ 5.87E-10
9.99E-13
1.27E-10
1.05E-12
3.33E-15
3.69E-08
/ 4.62
5.45
5.07
5.41
5.94
4.29
Photosystem II D2 protein / psbD / R.AFNPTQAEETYSMVTANR.F
R.AAEDPEFETFYTK.N
R.AWMAAQDQPHENLIFPEEVLPR.G
/ P48184
/ Zea mays
/ 2045.92
1547.69
2607.26
/ 2
2
3
/ 7.77E-15
4.20E-11
2.22E-15
/ 5.97
4.64
6.73
Photosystem Q(B) protein / psbA / K.FGQEEETYNIVAAHGYFGR.L
R.LIFQYASFNNSR.S
R.VINTWADIINR.A
/ P48183
/ Zea mays
/ 2188.00
1459.73
1314.71
/ 3
2
2
/ 4.80E-13
6.23E-07
4.62E-07
/ 5.17
4.12
3.84
PSII 22 kDa protein / psbS / R.FVDEEVTGLDKAVIQPGK.G
K.VEDGIFGTSGGIGFTKENELFVGR.V
R.GALGLSEGGPLFGFTK.S
/ Q6WFB1
/ Zea mays
/ 1945.03
2529.26
1550.82
/ 3
3
2
/ 5.00E-10
1.00E-08
5.00E-08
/ 4.07
2.61
3.22
7 / Chlorophyll a-b binding protein, chloroplastic, LHCII type I CAB / Lhcb1 / K.AKPAAASGSPWYGPDR.V
-.NGVQFGEAVWFK.-
/ P06671
P12328
/ Zea mays
Lemna gibba
/ 1630.79
1381.68
/ 2
2
/ 3.80E-09
2.32E-07
/ 3.84
3.39
Photosystem II type II chlorophyll a/b binding protein / Lhcb2 / K.VYPGGAFDPLGLADDPDTAAELK.V
-.NRELEVIHSR.-
K.SVPQSIWYGPDRPK.Y
/ O81608
P27520
Q41823
/ Sorghum bicolor
Pisum sativum
Zea mays
/ 2332.13
1252.67
1629.83
/ 2
2
2
/ 2.22E-15
6.94E-05
2.63E-05
/ 3.92
3.80
2.77
Photosystem II type III chlorophyll a/b binding protein / Lhcb3 / R.WAMLGALGCITPEVLEK.W
-.VDFKEPVWFK.-
/ A2YMN1
P27489
/ Oryza sativa subsp. indica
Solanum lycopersicum
/ 1887.97
1294.68
/ 2
2
/ 5.20E-07
4.02E-05
/ 5.36
2.74
Chlorophyll a/b-binding protein CP29 / Lhcb4 / K.STPLQPYSEVFGLQR.F
R.LYPGGSYFDPLGLAADPEKK.E
/ O24561
O24561
/ Zea mays
Zea mays
/ 1721.88
2138.08
/ 2
2
/ 3.29E-09
1.57E-08
/ 4.00
3.99
8 / Chlorophyll a/b-binding protein CP29 / Lhcb4 / -.NEAGGIIGTR.-
K.STPLQPYSEVFGLQR.F
R.LYPGGSYFDPLGLAADPEKK.E
K.PVEYLQFELDSLDQNLAK.N
K.GPLNNWATHLSDPLHTTIFDTFGGSS.-
. / O24561
/ Zea mays
/ 987.52
1721.88
2138.08
2122.07
2785.32
/ 2
3
2
3
3
/ 3.98E-03
1.27E-10
2.10E-08
7.26E-10
1.03E-06
/ 2.69
4.70
3.75
4.99
2.88
Chlorophyll a/b-binding apoprotein CP26 / Lhcb5 / R.RIYLPDGLLDR.S
R.SEVPEYLTGEVPGDYGYDPFGLGK.K
R.ITNGLDLEDKLHPGGPFDPLGLASDPDQAAILK.V
/ Q41746
Q41747
/ Zea mays
Zea mays
/ 1330.74
2589.20
3427.77
/ 2
2
4
/ 1.85E-06
6.95E-11
3.81E-04
/ 3.72
4.92
3.64
Chlorophyll a/b-binding apoprotein CP24 / Lhcb6 / R.DGVYIPDVDKLER.L
K.TAENFANFTGEQGYPGGK.F
/ Q41748
P27524
/ Zea mays
Solanum lycopersicum
/ 1518.77
1887.85
/ 2
2
/ 3.45E-07
6.62E-09
/ 2.69
5.01
Photosystem II type III chlorophyll a/b binding protein / Lhcb3 / R.WAMLGALGCITPEVLEK.W
K.VDFKEPVWFK.A
/ A2YMN1
P27489
/ Oryza sativa subsp. indica
Solanum lycopersicum
/ 1887.97
1294.68
/ 2
2
/ 3.63E-07
3.67E-05
/ 5.26
0.16
Chlorophyll a-b binding protein, chloroplastic, LHCII
type I CAB / Lhcb1 / R.VGGGPLGEGLDK.V
K.VAASGSPWYGPDR.V
/ A2XJ35
P12329
/ Oryza sativa subsp. Indica
Zea mays
/ 1098.57
1362.64
/ 2
2
/ 2.16E-05
1.45E-06
/ 3.50
3.41

a) MH+ Peptide masses; b) Z Charge value of each peptide; c) P(pep) Probability of finding a match as good as or better than the observed peptide match by chance; d) XCorr the cross-correlation value from the search, used to produce the final ranking of the candidate peptides in the search. XCorr values above 2.0 are indicative of a good correlation.