Table II

Experimental mass measurements of nuclear encoded thylakoid-associated proteins from A. thaliana

Protein aA. thaliana locusRetention timeIntact mass tag bCalculated intact mass cAmino-terminal CNBr or MSMS tag dCalculated amino-terminal CNBr tag eInternal CNBr tag f
minDaDaDaDa
PsbXIIIAt3g2105520.63347.63345.94N/D
PsaEIIAt2g2026026.410546.410546.93X
PsaEIVAt4g2875029.310469.810469.76X
PsaNVAt5g6404038.19702.79705.03X
PsbOIIIAt3g50820Fraction 4426571.712082.012082.05Y
PsaDIVAt4g0277045.117848.717847.39Y
PsbOVAt5g6657045.626566.726565.702082.012082.05Y
PsbPIAt1g0668047.120212.720212.416892.256890.38Y
PsbQIV1At4g2128048.716310.216309.57X
PsbQIVαAt4g0518050.616349.216349.51X
PsaHIIIAt3g1614057.610355.010355.82X
PsaHIAt1g5223057.610355.010354.79X
PetCIVAt4g0328058.819000.919000.681210.651210.61Y
AtpDIVAt4g0965072.420573.720570.59Y
PsbRIAt1g7904072.910340.910341.641859.001859.04Y
AtpCIVAt4g0464073.835709.335709.192626.582626.43Y
Lhca3IAt1g6152074.925058.625056.64Y
Lhcb1II2At2g34420Fraction 7624916.207830.77830.59Y
Lhcb1II1At2g34430Fraction 7624815.97Y
Lhca4IIIAt3g4747076.622256.022255.36N/D
Lhcb1At1g2993077.024906.924905.18Y
Lhcb1At1g2992077.024906.924905.18Y
Lhcb1At1g2991077.024906.924905.18Y
Lhcb2IIαAt2g0510079.124935.024930.187890.67890.72Y
Lhcb2IIIAt3g2769079.124935.024932.267890.67890.72Y
Lhca2IIIAt3g6147080.323201.823200.476250.46247.98Y
Lhcb6IAt1g1582080.823107.823106.32Y
Lhcb3IIAt5g5427083.124280.624280.656845.86845.57Y
Lhcb2IIβAt2g0507083.624945.024944.257890.67890.72Y
Lhcb5IVAt4g1034083.826449.026447.359630.99632.84Y
Lhcb4VAt5g0153083.928212.728212.07acVFGFGKY
PsbXcIIAt2g0652084.44183.74183.944182.364182.39Y
PetMIIAt2g2650098.74188.64188.89Y
PsbSIAt1g44575100.622457.622457.234900.754900.75Y
PsbWIIAt2g30570124.76004.06007.76N/D
  • a A. thaliana protein annotation using the standard gene names. Superscript roman numerals indicate the chromosome where the gene is located. For paralogs on the same chromosome, Arabic numerals indicate the long arm of the chromosome with 1 closest to the centromere, and lowercase Greek letters indicate the short arm of the chromosome with α closest to the centromere. See footnote 2 in the text concerning confusion about the use of psbX as a gene name.

  • b Intact mass tag of zero charge average mass determined by LCMS.

  • c Average zero charge mass predicted from translations of the indicated gene sequences using PeptideMass (us.expasy.org/tools/peptide-mass.html).

  • d Amino-terminal CNBr mass tags. All masses are monoisotopic unless underlined to indicate average mass. X indicates proteins that have no internal Met or have no CNBr peptides smaller than 10,000 Da. N/D, not detected. Amino termini confirmed by MSMS sequence data are listed.

  • e Predicted CNBr peptide mass calculated using MS-Digest program in ProteinProspector (prospector.ucsf.edu/ucsfhtml4.0/msdigest.htm). All masses are monoisotopic unless underlined to indicate average mass.

  • f Intact mass tags confirmed by internal CNBr mass tags other than or in addition to the amino-terminal CNBr mass tag.