University of Groningen Composition and structure of .... S3Alignment of the three different...

University of Groningen

Composition and structure of photosystem I in the moss Physcomitrella patensBusch, Andreas; Petersen, Jorgen; Webber-Birungi, Mariam T.; Powikrowska, Marta; Lassen,Laerke Marie Munter; Naumann-Busch, Bianca; Nielsen, Agnieszka Zygadlo; Ye, Juanying;Boekema, Egbert J.; Jensen, Ole NorregaardPublished in:Journal of Experimental Botany

DOI:10.1093/jxb/ert126

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Publication date:2013

Link to publication in University of Groningen/UMCG research database

Citation for published version (APA):Busch, A., Petersen, J., Webber-Birungi, M. T., Powikrowska, M., Lassen, L. M. M., Naumann-Busch, B., ...Jensen, P. E. (2013). Composition and structure of photosystem I in the moss Physcomitrella patens.Journal of Experimental Botany, 64(10), 2689-2699. DOI: 10.1093/jxb/ert126

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PpPsaD-1 MAALAATSAASIALAIPQASSGASTS-RSVNLRLSGIQGQKLAAVCNGSR

PpPsaD-2 MAALAATSAASVALIAPQASSGAAVSTRGVSLRVSSLQGQRLVAVCNSHR

PpPsaD-3 MAAFASTAATTLAIAAPSSVAASQLR-VNGSLKVSAFQGQKFAAACNGSR

PpPsaD-4 MAAIASTAITTVAIASPSSVAVSRPR-AAASLAISGFQGQKLASVCNGGR

***:*:*: :::*: *.: : : .* :*.:***::.:.**. *

PpPsaD-1 VVAKAAGAAPDATA-------EAPKGFTPPTLNADTPAPIFGGSTGGLLR

PpPsaD-2 VVA-KAAAAPDAAA-------EAPKGFTPPTLNADTPAPIFGGSTGGLLR

PpPsaD-3 LVMAQAGAAPDGVADQKPDAKEAPKGFTPPTLNADTPAPIFGGSTGGLLR

PpPsaD-4 VTMAQAGAVPDGVADRKPDAKEAPKGFTPPTLNADTPAPIFGGSTGGLLR

:. *.*.**..* *****************************

PpPsaD-1 KAQVEEFYVITWESPKEQIFEMPTGGAAIMRSGPNLLKLARKEQCLALGA




**************************************************

PpPsaD-1 RLRTKFKIQYQFYRVFPNGEVQYLHPKDGVYPEKVNAGRTAVGVNNRSIG

PpPsaD-2 RLRTKFKIQYQFYRVFPNGEVQYLHPKDGVYPEKVNAGRSPVGVNNRSIG



***************************************:.*********

PpPsaD-1 QNANPAELKFAHKQAYDL

Supplementary Material:

The composition and structure of photosystem I in the moss Physcomitrella patens

Andreas Busch, Jørgen Petersen, Mariam T. Webber-Birungi, Marta Powikrowska, Lærke

Marie Münter Lassen, Bianca Naumann-Busch, Agnieszka Zygadlo Nielsen, Juanying Ye,

Egbert J. Boekema, Ole Nørregaard Jensen, Christina Lunde, Poul Erik Jensen

Fig. S1 Sequence comparison of PsaD isoforms of P. patens

Alignment of full length protein sequences of the four different isoforms for PsaD of P.

patens. Sequence data were obtained from www.cosmoss.org, v1.6 PpPsaD-1

(Pp1s4_321V6.1), PpPsaD-2 (Pp1s77_69V6.1), PpPsaD-3 (Pp1s1_788V6.1), PpPsaD-4

(Pp1s107_188V6.1). Sequence alignment was created using ClustalW2

(http://www.ebi.ac.uk/Tools/msa/clustalw2/) with default settings.

Green indicates the chloroplast localization sequence as predicted by ChloroP

(Emanuelsson et al., 1999).

PpPsaD-1 QNANPAELKFAHKQAYDL

PpPsaD-2 KNANPAELKFAQKQAYDL

PpPsaD-3 KNANPAELKFAQKQAYDL

PpPsaD-4 KNANPAELKFAHKQAYDL

:**********:******

AtPsaF -MSLTIPAN------LVLNP------RSNKSLTQS---VPKSSARFVCSDD--KSSSSTP 42

GsPsaF ----------------------------------------------------------MM 2

CrPsaF -MALTMRN-------------------PAVKASSRVAPSSRRALRVACQAQ---KNETAS 37

S_PCC6803 ------------------------------------------------------------

PpPsaF-1 MASFTMAAA-IAPAGLVAPL--DLSSRTAISGSRASAFVKNSKARTTCSASSVDETTTVA 57

PpPsaF-2 MASVTMAAAAIAPVGLAANL--DLSSRAAISGTRTSMFVKNTKARTVCSAS-ADETATVA 57

PpPsaF-3 MASVTMAA--IAPAGLVAPLCKDVSSRTAISGARASVFVKSSKARIVCSTS-ADETSTVA 57

PpPsaF-4 ------------------------------------------------------------

AtPsaF QSMKAFSAAVALSSILLSAPMP---AVADISGLTPCKDSKQFAKREKQQIKKLESSLKLY 99

GsPsaF KINRFILYVILFSSILSFSTNN--LVQAEFNNLIPCKESKIFNKRLESTIKKLENKLSKY 60

CrPsaF KVGTALAASALAAAVSLSAPSA---AMADIAGLTPCSESKAYAKLEKKELKTLEKRLKQY 94

S_PCC6803 -MKHLLALLLAFTLWFNFAPSA---SADDFANLTPCSENPAYLAKSKNFLNTTN------ 50

PpPsaF-1 QAAGKFATALALAALVGGSDMVVPEAKADVAGLTPCKESKGFAKREKQEIKKLESRLKLY 117

PpPsaF-2 QTAGKFATALALAAIVGGSDMVVPEARADVAGLTPCKESKGFAKRQKQEIKKLESRLKLY 117

PpPsaF-3 ETAGKFATALALAAVVGSSDFVVPDARADVAGLTPCKESKGFAKRQKQEIKKLEGRLKLY 117

PpPsaF-4 ----------------------------------MSHRLQGFAKRQKQEIKKLEGRLKLY 26

. : :. ::. :

AtPsaF APESAPALALNAQIEKTKRRFDNYGKYGLLCGSDGLPHLIVNG----DQRHWGEFITPGI 155

GsPsaF EVGSSSYLAIKNTINKTNNRFHKYMESGVLCGKDGLPHLIADG----RWSHAGEFVIPSL 116

CrPsaF EADSAPAVALKATMERTKARFANYAKAGLLCGNDGLPHLIADPGLALKYGHAGEVFIPTF 154

S_PCC6803 DPNSG------------KIRAERYAS--ALCGPEGYPHLIVDG----RFTHAGDFLIPSI 92

PpPsaF-1 APDSAPALALNATIEKTKRRFAFYGNEGLLCGTDGLPHLIVDG----DQAHLGEFVYPGL 173

PpPsaF-2 APDSAPALAINATIEKTKRRFEFYGKQGLLCGTDGLPHLIVDG----DQAHLGEFVYPGL 173

PpPsaF-3 APDSAPALAINATIEKTKRRFEFYGNQGLLCGTDGLPHLIVDG----DQAHLGEFVYPGL 173

PpPsaF-4 APDSAPALAINATIEKTKRRFEFYGNQGLLCGTDGLPHLIVDG----DQAHLGEFVYPGL 82

*. : * * . *** :* ****.: * *:.. * :

AtPsaF LFLYIAGWIGWVGRSYLIAISGEKKPAMKEIIIDVPLASRIIFRGFIWPVAAYREFLNGD 215

GsPsaF LFIYISGWIGWVGRGYLSAIKNTNKAIENEIIIDVPLALKFMSSGFIWPLSALREYTKGD 176

CrPsaF GFLYVAGYIGYVGRQYLIAVKGEAKPTDKEIIIDVPLATKLAWQGAGWPLAAVQELQRGT 214

Fig. S2 Alignment of full length PsaF proteins from different species

Sequences for Physcomitrella are obtained from www.cosmoss.org, v1.6 PpPsaF-1

(Pp1s19_276V6.1), PpPsaF-2 (Pp1s345_25V6.1), PpPsaF-3 (Pp1s121_54V6.1), PpPsaF-4

(Pp1s80_23V6.1). Other sequences obtained from NCBI Arabidopsis thaliana :AtPsaF

(NP_174418), Galdieria sulphuraria GsPsaF (ADO32970.1), Chlamydomonas reinhardtii

CrPsaF (P12356), Synechocystis PCC6803 S_PCC6803 (P29256).

Alignment was created using ClustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/)

using default settings.

CrPsaF GFLYVAGYIGYVGRQYLIAVKGEAKPTDKEIIIDVPLATKLAWQGAGWPLAAVQELQRGT 214

S_PCC6803 LFLYIAGWIGWVGRSYLIEIRESKNPEMQEVVINVPLAIKKMLGGFLWPLAAVGEYTSGK 152

PpPsaF-1 VFLYIAGWIGWVGRAYLIDVRTSKKPTEKEIIIDVPLALRIMSKGLTWPVAAIGELRSGK 233

PpPsaF-2 VFLYIAGWIGWVGRAYLIDVRTSKKPTEKEIIIDVPLALRVMSKGFTWPLAAIGELRSGK 233

PpPsaF-3 VFLYIAGWIGWVGRAYLIDVRTSKKPTEKEIIIDVPLALRIMSKGLTWPVAAIGELRSGK 233

PpPsaF-4 VFLYIAGWIGWVGRAYLIDVRTSKKPTEKEIIIDVPLALRVMSKGFTWPLAAIGELRSGK 142

*:*::*:**:*** ** : :. :*::*:**** : * **::* * *

AtPsaF LIAKDV------- 221

GsPsaF LLMKDSEVTISPR 189

CrPsaF LLEKEENITVSPR 227

S_PCC6803 LVMKDSEIPTSPR 165

PpPsaF-1 LVEKSANITVSPR 246

PpPsaF-2 LVEKSGNITVSPR 246

PpPsaF-3 LVEKSSNITVSPR 246

PpPsaF-4 LVEKSANITVSPR 155

*: *.

Fig. S3 Alignment of the three different isoforms of PsaK of P. patens

Green indicates predicted chloroplast localization sequence (predicted by ChloroP,

Emanuelsson et al., 1999). Yellow indicates tryptic peptides that were identified with

MS/MS analysis (see Supplemental Table 1). Arginine and lysin residues in bold,

indicating potential tryptic cleavage sites.

Alignment was done with ClustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/) using

default settings. Sequences were obtained from www.cosmoss.org, V1.6

P.patens A.thaliana

Fig. S4: Traces of state transition experiment

Chlorophyll fluorescence measurements to assess the state 1/state 2 transition. State II was

induced by illumination of either Arabidopsis leafs or Physcomitrella protonema with blue

light for 20 min followed by a saturation pulse to determine the maximal fluorescence

(Fm2). State 1 was induced by illumination of the sample with far red light for 20 min

followed by a saturation pulse to determine the maximal fluorescence (Fm1).

Fig. S5: Expression data from GENEVESTIGATOR for selected isoforms

Visualization of the expression profile of isoforms of PSI core subunits using the

“Development” tool of Genevestigator (www.genevestigator.com). All 63 available

datasets for P. patens were included.

Protein name Area Relative intensity %

PsaA 5.39E+09 1.000000

PsaB 3.85E+09 0.715161

Lhca1 3.33E+09 0.617239

Lhca2 4.49E+09 0.833364

Lhca3 3.25E+09 0.603952

Lhca5 1.77E+06 0.000329

0,0

0,1

0,2

0,3

0,4

0,5

0,6

0,7

0,8

0,9

1,0

PsaA PsaB Lhca1 Lhca2 Lhca3 Lhca5

Re

lati

ve

in

ten

sity

Lhca5 1.77E+06 0.000329

Fig. S6 Label free quantification of PSI-LHCI proteins in P. patens

The label free quantification (Wong and Cagney 2010) were based on unique peptides from

PsaA, PsaB, Lhca1, Lhca2, Lhca3 and Lhca5 (including isoforms).

Materials and Methods:

The preliminary label free quantification was achieved using the Proteome Discoverer software (version 1.3.0.339).

Peptide areas were manually extracted from the data using only protein unique peptides as extraction criteria. Areas

from the different isoforms of Lhca1, Lhca2, Lhca3 and Lhca5 were pooled so only one Lhca1, Lhca2, Lhca3 and

Lhca5 appeared. The data analysis was based on the eleven raw files generated from the LC-MS/MS of peptides

extracted from the in-gel digested PSI proteins. The samples were analysed once and from only one replica and the

quantification data is therefore to be considered preliminary.

References:

Wong, J. W., and G. Cagney. 2010. An overview of label-free quantitation methods in proteomics by mass

spectrometry. Methods Mol Biol 604:273-83.

0

200

400

600

800

1000

1200

RP

KM

Figure S7: Expression profile of light harvesting proteins

in Physcomitrella patens.

Shown are reads per million per kb (RPKM) of the different

genes encoding light harvesting proteins of P. patens.

Samples are derived from P. patens cultures grown underSamples are derived from P. patens cultures grown under

standard conditions.

Material and Methods:

Six days old protonema was transferred on PhyB media and incubated for 8 hours under standard conditions (50µE

white light, 22°C). Subsequently protonemal tissue was harvested, excess water was removed by pressing the tissue

between tissue and the material was frozen in liquid nitrogen and stored at -80°C until further use. RNA was

isolated using the RNeasy Plant Mini Kit (Qiagen) following the suppliers manual.

Isolated RNA was send to GATC Biotech (Germany) for cDNA library synthesis and Illumina sequencing

(Illumina HiSeq 2000, 50bp single runs). Raw data were processed and mapped against the P. patens transcriptome

(P.patens.V1.2.2_CGI_transcripts.seq, downloaded from www.cosmoss.org) by GATC Biotech.

Fig. S8 Transmission electron microscopy and single particleFig. S8 Transmission electron microscopy and single particle

analysis of isolated PSII-LHCII complex of P. patens

(A) Averaged projection map of P. patens PSII core particles,

derived from 180 particles. (B) cyanobacterial PSII for

comparison, from a previous investigation (Kuhl et al. 1999).

Two-fold rotational symmetry was imposed on the images after

analysis.

Reference:

H. Kuhl, M. Rögner, J.F.L. van Breemen and E.J. Boekema (1999)

Localization of cyanobacterial PS II donor-side subunits by electron

microscopy and the supramolecular organization of PS II in the thylakoid

membrane. Eur. J. Biochem. 266, 453-460.

Fig. S9: Phylogenetic tree based on the protein sequence of cytochrome c6 sequences

Tree was constructed using ClustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/) using

default settings with sequences obtained from NCBI.

Table S1: Identified proteins and corresponding peptides. The table contains at the protein level: accession number for the protein,

probability based Mascot protein score. Protein sequence coverage, and molecular weight. At the peptide level: peptide sequence, protein

group accessions, possible modifications and individual probability based Mascot ion score.

Accession Protein Score Protein sequence Coverage % MW [kDa]

PhpapaCp040

(PsaB)

8274 22 82

Sequence Protein Group Accessions Modifications IonScore

IWFGIATAHDFESHDDmTEER PhpapaCp040 M17(Oxidation) 95

KEFGYSFPcDGPGR PhpapaCp040 C9(Carbamidomethyl)

89

QILIEPVFAQWIQSAHGK PhpapaCp040 88

IWFGIATAHDFESHDDMTEER PhpapaCp040 87

DKPVALSIVQAR PhpapaCp040 73

RIWFGIATAHDFESHDDMTEER PhpapaCp040 72

DYNPEQnKDNVLAR PhpapaCp040 N7(Deamidated) 71

EFGYSFPcDGPGR PhpapaCp040 C8(Carbamidomet

hyl)

66

TNFGIGHSMK PhpapaCp040;PhpapaCp039 64

TNFGIGHSmKEILEAHTPPGGR PhpapaCp040 M9(Oxidation) 64

EILEAHTPPGGR PhpapaCp040 64

WKDKPVALSIVQAR PhpapaCp040 62

RIWFGIATAHDFESHDDmTEER PhpapaCp040 M18(Oxidation) 60

LNHHLSGLFGVSSLAWTGHLVHVAIPESR PhpapaCp040 60

TnFGIGHSmK PhpapaCp040;PhpapaCp039 N2(Deamidated);

M9(Oxidation)

60

DYNPEQNKDNVLAR PhpapaCp040 55

TNFGIGHSmK PhpapaCp040;PhpapaCp039 M9(Oxidation) 50

WKPSVSWFK PhpapaCp040 48

TPLANLVR PhpapaCp040 54

GLSQDPTTR PhpapaCp040 46

TPLAnLVR PhpapaCp040 N5(Deamidated) 43

TnFGIGHSMK PhpapaCp040;PhpapaCp039 N2(Deamidated) 31

DYNPEQNK PhpapaCp040 26

LMPDKK PhpapaCp040 19

TNFGIGHSMKEILEAHTPPGGR PhpapaCp040 18

LmPDKK PhpapaCp040 M2(Oxidation) 29

PhpapaCp039

(PsaA)

9088 19 83


DYDPTTQYNNLLDR PhpapaCp039 107

DYDPTTQYNnLLDR PhpapaCp039 N10(Deamidated) 89

EILEAHKGPFTGEGHK PhpapaCp039 85

ImVEKDPVK PhpapaCp039 M2(Oxidation) 69

DLLAQLYPSFSK PhpapaCp039 68

TNFGIGHSMK PhpapaCp040;PhpapaCp039 64

TnFGIGHSmK PhpapaCp040;PhpapaCp039 N2(Deamidated); M9(Oxidation)

60

IMVEKDPVK PhpapaCp039 59

TNFGIGHSmKEILEAHK PhpapaCp039 M9(Oxidation) 56

TNFGIGHSMKEILEAHK PhpapaCp039 56

LLDAGVDPK PhpapaCp039 55

GPFTGEGHK PhpapaCp039 52

EIPLPHEFILNR PhpapaCp039 52

TNFGIGHSmK PhpapaCp040;PhpapaCp039 M9(Oxidation) 50

EIPLPHEFILnR PhpapaCp039 N11(Deamidated) 35

VAPAIQPR PhpapaCp039 52

DPVKTSFEK PhpapaCp039 50

LKVAPAIQPR PhpapaCp039 40

LIPDKAnLGFR PhpapaCp039 N7(Deamidated) 34

ALSIVQGR PhpapaCp039 49

FPcDGPGR PhpapaCp039 C3(Carbamidomethyl)

43

LIPDKANLGFR PhpapaCp039 39

WAKPGHFSR PhpapaCp039 36

TnFGIGHSMK PhpapaCp040;PhpapaCp039 N2(Deamidated) 31

EILEAHK PhpapaCp039 40

SPEPEVK PhpapaCp039 38

Pp1s89_62V6.1

(PpPsaH-1)

2638 44 15


SVYFDLGEIDNTTGNWDLYGNDDPNR Pp1s89_62V6.1;Pp1s206_11V6.1 93

FFETFAGAFTK Pp1s89_62V6.1;Pp1s206_11V6.1 79

QVPVMGPR Pp1s89_62V6.1 43

QVPVmGPR Pp1s89_62V6.1 M5(Oxidation) 24

YnGFQNK Pp1s89_62V6.1;Pp1s206_11V6.1 N2(Deamidated) 29

NGPKQVPVmGPR Pp1s89_62V6.1 M9(Oxidation) 14

YNGFQNK Pp1s89_62V6.1;Pp1s206_11V6.1 31

RGLLLK Pp1s89_62V6.1;Pp1s206_11V6.1;Pp1s267_72V6.1 21

Pp1s206_11V6.1

(PpPsaH-2)

2650 42 14


SVYFDLGEIDNTTGNWDLYGNDDPNR Pp1s89_62V6.1;Pp1s206_11V6.1 93

FFETFAGAFTK Pp1s89_62V6.1;Pp1s206_11V6.1 79

QAPIMGPR Pp1s206_11V6.1 36

QAPImGPR Pp1s206_11V6.1 M5(Oxidation) 39

YnGFQNK Pp1s89_62V6.1;Pp1s206_11V6.1 N2(Deamidated) 29

YNGFQNK Pp1s89_62V6.1;Pp1s206_11V6.1 31

RGLLLK Pp1s89_62V6.1;Pp1s206_11V6.1;Pp1s267_72V6.1 21

Pp1s4_321V6.1 (PpPsaD-1)

14898 69 22


KAQVEEFYVITWESPK Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 122

AQVEEFYVITWESPK Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 115

GFTPPTLnADTPAPIFGGSTGGLLR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 N8(Deamidated) 107

GFTPPTLNADTPAPIFGGSTGGLLR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 99

GFTPPTLNADTPAPIFGGSTGGLLRK Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 95

EQIFEmPTGGAAImR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 M6(Oxidation);

M14(Oxidation)

89

EQIFEMPTGGAAIMR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 79

AAGAAPDATAEAPK Pp1s4_321V6.1 75

KEQcLALGAR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 C4(Carbamidomet

hyl)

69

SIGQNANPAELK Pp1s4_321V6.1 69

DGVYPEKVNAGR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 63

TAVGVNNR Pp1s4_321V6.1 63

EQcLALGAR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 C3(Carbamidomet

hyl)

59

VFPNGEVQYLHPK Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 58

EQIFEMPTGGAAImR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 M14(Oxidation) 52

AQVEEFYVITWESPKEQIFEmPTGGAAImR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 M21(Oxidation);

M29(Oxidation)

51

SIGQnANPAELK Pp1s4_321V6.1 N5(Deamidated) 48

DGVYPEKVnAGR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 N9(Deamidated) 45

FKIQYQFYR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 40

VFPnGEVQYLHPK Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 N4(Deamidated) 40

KAqVEEFYVITWESPK Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 Q3(Deamidated) 27

SGPNLLKLAR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 43

TAVGVnNR Pp1s4_321V6.1 N6(Deamidated) 60

IQYQFYR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 39

DGVYPEK Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 50

KEqcLALGAR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 Q3(Deamidated);

C4(Carbamidomet

hyl)

49

SGPNLLK Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 42

SGPnLLK Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 N4(Deamidated) 46

EqcLALGAR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 Q2(Deamidated);

C3(Carbamidomet

hyl)

18

Pp1s77_69V6.1

(PpPsaD-2)

14002 68 22








M14(Oxidation)

89

AAAAPDAAAEAPK Pp1s77_69V6.1 79


KEQcLALGAR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 C4(Carbamidomethyl)

69

SIGKnANPAELK Pp1s1_788V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 N5(Deamidated) 67


EQcLALGAR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 C3(Carbamidomet

hyl)

59



AQVEEFYVITWESPKEQIFEmPTGGAAImR Pp1s1_788V6.1;Pp1s4_321V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 M21(Oxidation);

M29(Oxidation)

51


SIGKNANPAELK Pp1s1_788V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 42




SPVGVNNR Pp1s1_788V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 51

SPVGVnNR Pp1s1_788V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 N6(Deamidated) 50





C4(Carbamidomet

hyl)

49


nANPAELK Pp1s1_788V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 N1(Deamidated) 36


NANPAELK Pp1s1_788V6.1;Pp1s77_69V6.1;Pp1s107_188V6.1 33


C3(Carbamidomethyl)

18

Pp1s101_2V6.1

(PpPsaE-3)

3318 55 14


ESYWFNDTGKVVAVDQAPGVR Pp1s101_2V6.1;Pp1s319_36V6.1;Pp1s334_17V6.1 75

RESYWFnDTGK Pp1s101_2V6.1;Pp1s319_36V6.1;Pp1s334_17V6.1 N7(Deamidated) 65

AEEAAAAPPAK Pp1s101_2V6.1 61

AEEAAAAPPAKK Pp1s101_2V6.1 60

ESYWFnDTGK Pp1s101_2V6.1;Pp1s319_36V6.1;Pp1s334_17V6.1 N6(Deamidated) 60

RESYWFNDTGK Pp1s101_2V6.1;Pp1s319_36V6.1;Pp1s334_17V6.1 59

KEAQPVIGPK Pp1s101_2V6.1 59

KEAqPVIGPK Pp1s101_2V6.1 Q4(Deamidated) 59

VVAVDQAPGVR Pp1s101_2V6.1;Pp1s319_36V6.1;Pp1s334_17V6.1 57

EAQPVIGPK Pp1s101_2V6.1 57

ESYWFNDTGK Pp1s101_2V6.1;Pp1s319_36V6.1;Pp1s334_17V6.1 55

VVAVDqAPGVR Pp1s101_2V6.1;Pp1s319_36V6.1;Pp1s334_17V6.1 Q6(Deamidated) 47

FDKVNYAGVSTNNYSPDELEQSA Pp1s101_2V6.1 56

FDKVNYAGVSTNnYSPDELEQSA Pp1s101_2V6.1 N13(Deamidated) 35

VVAVDQAPGVRYPVVVR Pp1s101_2V6.1;Pp1s319_36V6.1;Pp1s334_17V6.1 33

YPVVVRFDK Pp1s101_2V6.1;Pp1s319_36V6.1;Pp1s334_17V6.1 36

VNYAGVSTNNYSPDELEQSA Pp1s101_2V6.1 34

VNYAGVSTnNYSPDELEQSA Pp1s101_2V6.1 N9(Deamidated) 23

YPVVVR Pp1s101_2V6.1;Pp1s319_36V6.1;Pp1s334_17V6.1 32

Pp1s319_36V6.1 (PpPsaE-2)

3356 57 14



AEDAAAAPTPAPPVEK Pp1s319_36V6.1 74

FDKVNYAGVSTNNYSPDELEAAE Pp1s319_36V6.1;Pp1s334_17V6.1 67






EVKPVIGPK Pp1s319_36V6.1 50


FDKVNYAGVSTnNYSPDELEAAE Pp1s319_36V6.1;Pp1s334_17V6.1 N12(Deamidated) 40

VNYAGVSTnNYSPDELEAAE Pp1s319_36V6.1;Pp1s334_17V6.1 N9(Deamidated) 37

VNYAGVSTNNYSPDELEAAE Pp1s319_36V6.1;Pp1s334_17V6.1 34



EVKPVIGPKR Pp1s319_36V6.1 37


Pp1s334_17V6.1 (PpPsaE-1)

3645 57 14



FDKVNYAGVSTNNYSPDELEAAE Pp1s319_36V6.1;Pp1s334_17V6.1 67


AEEAAAPGAPVAPVK Pp1s334_17V6.1 64

AEEAAAPGAPVAPVKEEAKPVIGPK Pp1s334_17V6.1 62

EEAKPVIGPK Pp1s334_17V6.1 60






FDKVNYAGVSTnNYSPDELEAAE Pp1s319_36V6.1;Pp1s334_17V6.1 N12(Deamidated) 40

VNYAGVSTnNYSPDELEAAE Pp1s319_36V6.1;Pp1s334_17V6.1 N9(Deamidated) 37

VNYAGVSTNNYSPDELEAAE Pp1s319_36V6.1;Pp1s334_17V6.1 34


EEAKPVIGPKR Pp1s334_17V6.1 46



Pp1s429_33V6.2

(Lhca3.2)

6405 38 34


FAmLGAAGAIAPEVLGR Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1

M3(Oxidation) 116

FAMLGAAGAIAPEVLGR Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33V6.1

93

FLGGSGNPAYPGGPIFNFLGFGK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1;Pp1s197_123V6.1

77

AQDYYKPGSMGK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33V6.1;Pp1s197_123V6.1

62

AQDYYKPGSmGK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1;Pp1s197_123V6.1

M10(Oxidation) 54

RAQDYYKPGSmGK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33V6.1;Pp1s197_123V6.1

M11(Oxidation) 48

RAQDYYKPGSMGK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1;Pp1s197_123V6.1

43

LAmmAVLGYFTQAIFTGVGPFQNLLDHLADPVHNNVLTNLK

Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33V6.1

M3(Oxidation); M4(Oxidation)

32

NEKELQELK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1

59

nEKELQELK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33V6.1

N1(Deamidated) 56

QYFLGLEK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1;Pp1s197_123V6.1

43

nLIFASK Pp1s429_33V6.2 N1(Deamidated) 43

NLIFASK Pp1s429_33V6.2 32

ELQELK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33V6.1

37

ELQELKVK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1

10

Pp1s197_123V6.1

(Lhca3.3)

3349 42 31


FAmLGAAGAIAPEILGR Pp1s197_123V6.1 M3(Oxidation) 100

FAMLGAAGAIAPEILGR Pp1s197_123V6.1 88

FLGGSGNPAYPGGPIFNFLGFGK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1;Pp1s197_123V6.1

77

AQDYYKPGSMGK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1;Pp1s197_123V6.1

62

AQDYYKPGSmGK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1;Pp1s197_123V6.1

M10(Oxidation) 54

AQLSPTGGSK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s197_123V6.1 52

RAQDYYKPGSmGK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1;Pp1s197_123V6.1

M11(Oxidation) 48

RAQDYYKPGSMGK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1;Pp1s197_123V6.1

43

LAmmAVLGYFIQAIFTGVGPFQNLLDHLADPVH

nNVLTNLK

Pp1s197_123V6.1 M3(Oxidation);

M4(Oxidation);

N34(Deamidated)

23

RSLIFASK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s197_106V6.1;Pp1s197_12

3V6.1

37

SLIFASK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s197_106V6.1;Pp1s197_12

3V6.1

44

QYFLGLEK Pp1s214_86V6.1;Pp1s214_87V6.2;Pp1s214_87V6.1;Pp1s429_33V6.2;Pp1s429_33

V6.1;Pp1s197_123V6.1

43

Pp1s345_25V6.1

(PpPsaF-2)

8220 32 26


KPTEKEIIIDVPLALR Pp1s345_25V6.1;Pp1s19_276V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1 132

LYAPDSAPALAInATIEK Pp1s345_25V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1;Pp1s19_276V6.1 N13(Deamidated) 110

LYAPDSAPALAINATIEK Pp1s19_276V6.1;Pp1s345_25V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1 109

LKLYAPDSAPALAINATIEK Pp1s345_25V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1;Pp1s19_276V6.1 91

GFTWPLAAIGELR Pp1s345_25V6.1;Pp1s80_23V6.1 86

LYAPDSAPALAINATIEKTK Pp1s345_25V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1;Pp1s19_276V6.1 81

SGnITVSPR Pp1s345_25V6.1 N3(Deamidated) 67

LVEKSGNITVSPR Pp1s345_25V6.1 66

SGNITVSPR Pp1s345_25V6.1 57

EIIIDVPLALR Pp1s345_25V6.1;Pp1s19_276V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1 53

LKLYAPDSAPALAInATIEK Pp1s345_25V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1;Pp1s19_276V6.1 N15(Deamidated) 35

AYLIDVR Pp1s345_25V6.1;Pp1s19_276V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1 47

RFEFYGK Pp1s345_25V6.1 24

FEFYGK Pp1s345_25V6.1 19

Pp1s54_165V6.1

(PpPsaL-1)

2737 10 23


EGEPSKAPSLTLTGR Pp1s54_165V6.1 77

TAVAPLLR Pp1s15_408V6.1;Pp1s41_267V6.1;Pp1s54_165V6.1 61

APSLTLTGR Pp1s15_408V6.1;Pp1s41_267V6.1;Pp1s54_165V6.1 54

Pp1s121_54V6.1 8481 27 26


KPTEKEIIIDVPLALR Pp1s345_25V6.1;Pp1s19_276V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1 132

LYAPDSAPALAInATIEK Pp1s345_25V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1;Pp1s19_276V6.1 N13(Deamidated) 110

LYAPDSAPALAINATIEK Pp1s19_276V6.1;Pp1s345_25V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1 109

LKLYAPDSAPALAINATIEK Pp1s345_25V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1;Pp1s19_276V6.1 91

LYAPDSAPALAINATIEKTK Pp1s345_25V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1;Pp1s19_276V6.1 81

GLTWPVAAIGELR Pp1s19_276V6.1;Pp1s121_54V6.1 68

SSNITVSPR Pp1s121_54V6.1 59

EIIIDVPLALR Pp1s345_25V6.1;Pp1s19_276V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1 53

LKLYAPDSAPALAInATIEK Pp1s345_25V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1;Pp1s19_276V6.1 N15(Deamidated) 35

AYLIDVR Pp1s345_25V6.1;Pp1s19_276V6.1;Pp1s80_23V6.1;Pp1s121_54V6.1 47

SSnITVSPR Pp1s121_54V6.1 N3(Deamidated) 45

Pp1s241_66V6.1

(PpPsaF-3)

3761 28 29


WAmLGAAGIFIPEALTK Pp1s241_66V6.1;Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 M3(Oxidation) 92

RWADIINPGcVNVDPVFPnNK Pp1s241_66V6.1 C10(Carbamidome

thyl);

N19(Deamidated)

77

WADIINPGcVNVDPVFPnNK Pp1s241_66V6.1 C9(Carbamidomethyl);

N18(Deamidated)

77

WFVQAELVHcR Pp1s241_66V6.1;Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 C10(Carbamidomethyl)

75

WADIINPGcVNVDPVFPNNK Pp1s241_66V6.1 C9(Carbamidomet

hyl)

74

LTGTDVGYPGGLWFDPLGWGQTGDAAK Pp1s241_66V6.1 69

RWADIINPGcVNVDPVFPNNK Pp1s241_66V6.1 C10(Carbamidome

thyl)

68

RWADIInPGcVnVDPVFPNNK Pp1s241_66V6.1 N7(Deamidated); C10(Carbamidome

thyl);

N12(Deamidated)

34

WAMLGAAGIFIPEALTK Pp1s241_66V6.1;Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 56

WFVqAELVHcR Pp1s241_66V6.1;Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 Q4(Deamidated); C10(Carbamidome

thyl)

24

WADIInPGcVnVDPVFPNNK Pp1s241_66V6.1 N6(Deamidated);

C9(Carbamidomethyl);

N11(Deamidated)

20

Pp1s158_109V6.1 5785 51 26

(Lhca1.1)


THLADPWHNTIAHVIIPR Pp1s158_109V6.1;Pp1s161_32V6.1 110

KYPGGAFDPLGFSK Pp1s158_109V6.1 97

YPGGAFDPLGFSK Pp1s158_109V6.1 85

nGEPDPEKR Pp1s158_109V6.1 N1(Deamidated) 74

THLADPWHnTIAHVIIPR Pp1s161_32V6.1;Pp1s158_109V6.1 N9(Deamidated) 72

WAmLAVPGVLIPEALGYGNWVSAQK Pp1s158_109V6.1;Pp1s247_7V6.1 M3(Oxidation) 71

WAATPGGQATYLGNPVPWGNLPVILAIEFLAIA

FAESQR

Pp1s158_109V6.1 67

NGEPDPEKR Pp1s158_109V6.1 59

ESELIHAR Pp1s158_109V6.1;Pp1s161_32V6.1;Pp1s161_32V6.2;Pp1s247_7V6.1 54

FKESELIHAR Pp1s158_109V6.1;Pp1s161_32V6.1;Pp1s161_32V6.2;Pp1s247_7V6.1 53

GANLEELKLK Pp1s158_109V6.1;Pp1s161_32V6.1;Pp1s161_32V6.2;Pp1s247_7V6.1 58

nGEPDPEK Pp1s158_109V6.1 N1(Deamidated) 47

NGEPDPEK Pp1s158_109V6.1 47

GANLEELK Pp1s158_109V6.1;Pp1s161_32V6.1;Pp1s161_32V6.2;Pp1s247_7V6.1 50

GAnLEELK Pp1s158_109V6.1;Pp1s161_32V6.1;Pp1s161_32V6.2;Pp1s247_7V6.1 N3(Deamidated) 37

Pp1s161_32V6.1 (Lhca1.2)

5069 32 26


THLADPWHNTIAHVLIPR Pp1s158_109V6.1;Pp1s161_32V6.1 110

KYPGGPFDPLGFSK Pp1s161_32V6.1;Pp1s161_32V6.2 88

LALVAFLGFVVQAVAYPGTGPLENLK Pp1s161_32V6.1 85

YPGGPFDPLGFSK Pp1s161_32V6.1;Pp1s161_32V6.2 80

THLADPWHnTIAHVLIPR Pp1s161_32V6.1;Pp1s158_109V6.1 N9(Deamidated) 72






Pp1s247_7V6.1

(Lhca1.3)

2997 52 26


THLADPWHNTIANILIPR Pp1s247_7V6.1 99

YPGGAFDPmGFSK Pp1s247_7V6.1 M9(Oxidation) 72

YPGGAFDPMGFSK Pp1s247_7V6.1 72

WAmLAVPGVLIPEALGYGNWVSAQK Pp1s158_109V6.1;Pp1s247_7V6.1 M3(Oxidation) 71

KYPGGAFDPmGFSK Pp1s247_7V6.1 M10(Oxidation) 62

KYPGGAFDPMGFSK Pp1s247_7V6.1 59

THLADPWHnTIANILIPR Pp1s247_7V6.1 N9(Deamidated) 56






LALVAFLGFAIQAIAYPGTGPLENLK Pp1s247_7V6.1 45

mASAmATAAAQATRLVTGVAAAqK Pp1s247_7V6.1 M1(Oxidation); M5(Oxidation);

Q23(Deamidated)

13

PhpapaCp076 (PpPsaC)

5155 99 9


cESAcPTDFLSVR PhpapaCp076 C1(Carbamidomethyl);

C5(Carbamidomet

hyl)

95

AcPTDVLEMVPWDGcK PhpapaCp076 C2(Carbamidomethyl);

C15(Carbamidome

thyl)

93

AcPTDVLEmVPWDGcK PhpapaCp076 C2(Carbamidomet

hyl);

M9(Oxidation); C15(Carbamidome

thyl)

72

IYDTcIGcTQcVR PhpapaCp076 C5(Carbamidomethyl);

C8(Carbamidomet

hyl); C11(Carbamidome

thyl)

71

IYDTcIGcTqcVR PhpapaCp076 C5(Carbamidomet

hyl); C8(Carbamidomet

hyl);

Q10(Deamidated); C11(Carbamidome

thyl)

70

ASQIASAPR PhpapaCp076 60

TEDcVGcK PhpapaCp076 C4(Carbamidomet


58

hyl)

RcESAcPTDFLSVR PhpapaCp076 C2(Carbamidomet


hyl)

47

TEDcVGcKR PhpapaCp076 C4(Carbamidomethyl);

C7(Carbamidomet

hyl)

47

VYLGAETTR PhpapaCp076 43

VYLGAETTRSmGLAY PhpapaCp076 M11(Oxidation) 41

AHSVKIYDTcIGcTQcVR PhpapaCp076 C10(Carbamidome

thyl);

C13(Carbamidomethyl);

C16(Carbamidome

thyl)

28

Pp1s78_205V6.1

(PsaG-2)

1515 33 17


QGLPEQNGVTHYDAGDTR Pp1s78_205V6.1 113

QGLPEQnGVTHYDAGDTR Pp1s78_205V6.1 N7(Deamidated) 94

AQEVVGmLK Pp1s78_205V6.1 M7(Oxidation) 48

FVFLPFQR Pp1s78_205V6.1;Pp1s83_246V6.1 43

AQEVVGMLK Pp1s78_205V6.1 41

FVFLPFqR Pp1s78_205V6.1;Pp1s83_246V6.1 Q7(Deamidated) 39

LDSVAmR Pp1s78_205V6.1 M6(Oxidation) 11

LDSVAmRSNSFASqTAIcK Pp1s78_205V6.1 M6(Oxidation);

Q14(Deamidated);

C18(Carbamidomethyl)

11

Pp1s83_246V6.1

(PpPsaG-1

4363 23 16


QGLPVQNGVTHFDAGDSR Pp1s83_246V6.1 112

QGLPVQnGVTHFDAGDSR Pp1s83_246V6.1 N7(Deamidated) 86

AQEVTSFLK Pp1s83_246V6.1 56

qGLPVQnGVTHFDAGDSR Pp1s83_246V6.1 Q1(Deamidated);

N7(Deamidated)

56

AqEVTSFLK Pp1s83_246V6.1 Q2(Deamidated) 49

FVFLPFQR Pp1s78_205V6.1;Pp1s83_246V6.1 43

FVFLPFqR Pp1s78_205V6.1;Pp1s83_246V6.1 Q7(Deamidated) 39

Pp1s284_6V6.1 (Lhca5)

503 11 59


TDIPVWFEAGATK Pp1s284_6V6.1 91

FAmAGVAGILFTDLLR Pp1s284_6V6.1 M3(Oxidation) 91

WYVQAELVHSR Pp1s284_6V6.1 52

TGPIENLLTHLSDPVHNTIIQR Pp1s284_6V6.1 19

Pp1s330_37V6.1

(Lhca2.2)

3724 37 29



WFVQAELVHcR Pp1s241_66V6.1;Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 C10(Carbamidomethyl)

75

WADIVNPGcVNVDPVFPNNK Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 C9(Carbamidomet

hyl)

72

RWADIVNPGcVNVDPVFPnNK Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 C10(Carbamidomethyl);

N19(Deamidated)

58

WADIVNPGcVNVDPVFPnNK Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 C9(Carbamidomet

hyl);

N18(Deamidated)

58

RWADIVNPGcVNVDPVFPNNK Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 C10(Carbamidomethyl)

57

APEWLDGSLPGDFGFDPLGLGSDPELLK Pp1s330_37V6.1 39


LTGTDVGYPGGLWFDPLGWGQTK Pp1s330_37V6.1 47

WFVqAELVHcR Pp1s241_66V6.1;Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 Q4(Deamidated); C10(Carbamidome

thyl)

24

Pp1s651_2V6.1 (Lhca2.4)

3673 25 30



WFVQAELVHcR Pp1s241_66V6.1;Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 C10(Carbamidome

thyl)

75

WADIVNPGcVNVDPVFPNNK Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 C9(Carbamidomethyl)

72

RWADIVNPGcVNVDPVFPnNK Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 C10(Carbamidome

thyl);

N19(Deamidated)

58

WADIVNPGcVNVDPVFPnNK Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 C9(Carbamidomet

hyl); N18(Deamidated)

58

RWADIVNPGcVNVDPVFPNNK Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 C10(Carbamidome

thyl)

57

mGILNTPSWTVAGDADYFTDK Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 M1(Oxidation) 28


WFVqAELVHcR Pp1s241_66V6.1;Pp1s330_37V6.1;Pp1s651_2V6.2;Pp1s651_2V6.1;Pp1s651_2V6.3 Q4(Deamidated);

C10(Carbamidome

thyl)

24

Pp1s248_61V6.2

PpPsaO-2)

27 9 15


GRQDGYWN Pp1s248_61V6.2 22

DWLRK Pp1s248_61V6.2 12

Accession Description Score Coverage MW [kDa]

Pp1s1_788V2.1

(PpPsaD-3)

Phypa_110797 psi reaction center subunit ii 11786 95 18





AQAGAAPDGVADQKPDAK Pp1s1_788V2.1 97



M14(Oxidation)

75



KEQcLALGAR Pp1s107_188V2.1;Pp1s77_69V2.1;Pp1s4_321V2.1;Pp1s1_788V2.1 C4(Carbamidomethyl) 66

SPVGVnNR Pp1s107_188V2.1;Pp1s77_69V2.1;Pp1s1_788V2.1 N6(Deamidated) 61




SPVGVNNR Pp1s107_188V2.1;Pp1s77_69V2.1;Pp1s1_788V2.1 57

KAQVEEFYVITWESPKEQIFEmPTGGAAImR Pp1s107_188V2.1;Pp1s77_69V2.1;Pp1s4_321V2.1;Pp1s1_788V2.1 M22(Oxidation);

M30(Oxidation)

46

SIGKnANPAELK Pp1s107_188V2.1;Pp1s77_69V2.1;Pp1s1_788V2.1 N5(Deamidated) 45



C4(Carbamidomethyl)

44

SIGKNANPAELK Pp1s107_188V2.1;Pp1s77_69V2.1;Pp1s1_788V2.1 44




EQcLALGAR Pp1s107_188V2.1;Pp1s77_69V2.1;Pp1s4_321V2.1;Pp1s1_788V2.1 C3(Carbamidomethyl) 38

AQVEEFYVITWESPKEQIFEmPTGGAAImR Pp1s107_188V2.1;Pp1s77_69V2.1;Pp1s4_321V2.1;Pp1s1_788V2.1 M21(Oxidation); M29(Oxidation)

37






NANPAELK Pp1s107_188V2.1;Pp1s77_69V2.1;Pp1s1_788V2.1 27

nANPAELK Pp1s107_188V2.1;Pp1s77_69V2.1;Pp1s1_788V2.1 N1(Deamidated) 34


C3(Carbamidomethyl)

18

NANPAELKFAQKQAYDL Pp1s77_69V2.1;Pp1s1_788V2.1 12

Table S2: Photosynthetic parameters derived from chlorophyll-a fluorescence measurements.

PSII photochemistry (Fv/Fm), Excitation pressure (1-qL) and non-photochemical quenching (NPQ)

measured under PSII (blue) and PSI (far red) light. The values are averages ± S.D. Photosynthetic

parameters were calculated using the following equations, Fv/Fm=(Fm-F0)/Fm, NPQ = (Fm–

Fm’)/Fm’, qL=(Fm’-F)/(Fm’-F0’)xF0’/F. F0’ was calculated using the following equation:

F0’=F0/(Fv/Fm+F0/Fm’).

A. thaliana (n=3) P. patens (n=4)

Fv/Fm 1-qL NPQ Fv/Fm 1-qL NPQ

darkness 0.781±0.009 0.000±0.000 0.000±0.000 0.691±0.034 0.000±0.000 0.000±0.000

after 20min blue light

0.633±0.006 0.354±0.032 0.338±0.040 0.558±0.040 0.350±0.004 0.158±0.009

after 20min far red light

0.762±0.008 -0.025±0.034 0.147±0.032 0.685±0.030 0.004±0.030 0.027±0.009

(Fm1-Fm2)/Fm2 = 0.167±0.005 (Fm1-Fm2)/Fm2 = 0.128±0.005

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