Th of which can oxidatively modify proteins. To alleviate this problem the polyacrylamide gels used in this study were thoroughly degassed and photopolymerized with flavin mononucleotide, diphenyliodonium chloride and sodium toluenesulfinic acid [46]. Additionally, the 
cathode buffer contained thioglycolate [47]. This electrophoretic system had been shown to completlyOxidized Amino Acids on the Reducing Side of PS IIeliminate artifactual electrophoresis-associated oxidative modifications of cytochrome c [47] and greatly minimize apparent electrophoresis-induced oxidative modifications in PS II (see [20] Fig. S1). Subsequent to electrophoresis, the protein and peptide samples were maintained under reducing conditions (presence of dithiothreitol and/or low pH) to minimize artifactual oxidative modifications. Staining was performed in the presence of acetic acid, the excised protein bands were reduced with dithiothreitol (and then blocked with iodoacetic acid), and after tryptic digestion the peptides were brought to 0.1 formic acid and frozen at 280uC. Reversed phase HPLC was performed in the presence 
of 0.1 formic acid. The Epigenetics sheath and auxiliary gas for electrospray ionization was N2 [20].Supporting InformationFigure S1 Mass Spectrometry Data from the 15900046 Unmodified Peptide. 235AFNPTQAEETYSMVTAN252R and the Oxidatively Modified Peptide 235AFN238P+16 239T+16 QA242E30 ETYSM+16 VTAN252R of the D2 Protein A. Top, spectrum of the CID dissociation of the unmodified peptide 235AFNPTQAEETYSMVTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions Epigenetic Reader Domain generated from this peptide sequence. Ions identified in the CID spectrum (above) are shown in red. The b’++, b’+ y’++ and y’+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. B. Top, spectrum of the CID dissociation of the modified 235AFN238P+16 239T+16 QA242E-30 ETYSM+16 VTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum are shown in red. The b’++, b’+ y’++ and y’+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. The p values for the unmodified and modified peptide were 10213 and 10214, respectively. (DOCX)Figure S2 Mass Spectrometry Data from the Unmodified Peptide. 239FGQEEETYNIHAAHGYFG257R and the Oxidatively Modified Peptide 239F+16 G241Q+14 242E-30 EETYNIHAAHGYFG257R of the D1 Protein A. Top, spectrum of the CID dissociation of the unmodified peptide 239FGQEEETYNIHAAHGYFG257R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum (above) are shown in red. The b’++, b’+ y’++ and y’+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. B. Top, spectrum of the CID dissociation of the modified G241Q+14 242E-30 EETYNIHAAHGYFG257R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum are shown in red. The b’++, b’+ y’++ and y’+ ions are generated by the neutral 26001275 loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. The p values for the.Th of which can oxidatively modify proteins. To alleviate this problem the polyacrylamide gels used in this study were thoroughly degassed and photopolymerized with flavin mononucleotide, diphenyliodonium chloride and sodium toluenesulfinic acid [46]. Additionally, the cathode buffer contained thioglycolate [47]. This electrophoretic system had been shown to completlyOxidized Amino Acids on the Reducing Side of PS IIeliminate artifactual electrophoresis-associated oxidative modifications of cytochrome c [47] and greatly minimize apparent electrophoresis-induced oxidative modifications in PS II (see [20] Fig. S1). Subsequent to electrophoresis, the protein and peptide samples were maintained under reducing conditions (presence of dithiothreitol and/or low pH) to minimize artifactual oxidative modifications. Staining was performed in the presence of acetic acid, the excised protein bands were reduced with dithiothreitol (and then blocked with iodoacetic acid), and after tryptic digestion the peptides were brought to 0.1 formic acid and frozen at 280uC. Reversed phase HPLC was performed in the presence of 0.1 formic acid. The sheath and auxiliary gas for electrospray ionization was N2 [20].Supporting InformationFigure S1 Mass Spectrometry Data from the 15900046 Unmodified Peptide. 235AFNPTQAEETYSMVTAN252R and the Oxidatively Modified Peptide 235AFN238P+16 239T+16 QA242E30 ETYSM+16 VTAN252R of the D2 Protein A. Top, spectrum of the CID dissociation of the unmodified peptide 235AFNPTQAEETYSMVTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum (above) are shown in red. The b’++, b’+ y’++ and y’+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. B. Top, spectrum of the CID dissociation of the modified 235AFN238P+16 239T+16 QA242E-30 ETYSM+16 VTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum are shown in red. The b’++, b’+ y’++ and y’+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. The p values for the unmodified and modified peptide were 10213 and 10214, respectively. (DOCX)Figure S2 Mass Spectrometry Data from the Unmodified Peptide. 239FGQEEETYNIHAAHGYFG257R and the Oxidatively Modified Peptide 239F+16 G241Q+14 242E-30 EETYNIHAAHGYFG257R of the D1 Protein A. Top, spectrum of the CID dissociation of the unmodified peptide 239FGQEEETYNIHAAHGYFG257R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum (above) are shown in red. The b’++, b’+ y’++ and y’+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. B. Top, spectrum of the CID dissociation of the modified G241Q+14 242E-30 EETYNIHAAHGYFG257R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum are shown in red. The b’++, b’+ y’++ and y’+ ions are generated by the neutral 26001275 loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. The p values for the.