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. 2011 Oct 7;23(10):3727–3744. doi: 10.1105/tpc.111.087403

Table 1.

Identification of Actin, VDAC, and ADP/ATP Carrier Protein (ANT) as Well-Bound DNA Binding Proteins in Mitochondria from Mung Bean Seedlings

Accession No. Protein Name Mass Scorea emPAIb Coverage (%)c Peptide Scored Peptide Sequence
Q9SRH5 VDAC1 29,482 3,705 0.3 6.9 40.71 NITTDLK
94.84 SFFTISGEVDTK
P42054 VDAC 29,596 1,315 2.26 12.7 40.71 NITTDLK
72.28 GPGLYTDIGK
65.11 VKGPGLYTDIGK
56.45 GELFLGDVNTQLK
80.46 KGELFLGDVNTQLK
58.22 KGELFLGDVNTQLKNK
O22342 ADP/ATP carrier protein 1 42,264 217 0.45 10.9 48.74 SDGIAGLYR
70.78 QFNGLVDVYR
55.7 LLIQNQDEMIK
69.61 YFPTQALNFAFK
P31167 ADP/ATP carrier protein 1 41,589 145 0.6 15 40.16 TAAAPIER
49.6 GNTANVIR
49.02 LQLIVFGK
62.48 QFDGLVDVYR
55.29 LLIQNQDEMIK
58.44 YFPTQALNFAFK
P0C539 Actin-2 41,907 234 0.32 17.8 99.11 SYELPDGQVITIGAER
46.88 DLYGNIVLSGGSTMFPGIADR
67.62 TTGIVLDSGDGVSHTVPIYEGYALPHAILR
P93372 Actin-66 (fragment) 37,357 138 0.23 13.7 47.96 SYELPDGQVITIGSER
67.62 TTGIVLDSGDGVSHTVPIYEGYALPHAILR
P30171 Actin-97 41,870 92 0.32 16.2 44.09 GYSFTTSAER
51.26 DLYGNIVLSGGTTMFPGIADR
76.38 TTGIVLDSGDGVSHTVPIYEGYALPHAILR
Q9LQ81 Actin-depolymerizing factor 10 16,513 124 0.26 8.6 74.27 IFFIAWSPDTSR

VDAC, ADP/ATP carrier protein, and actin were present in the native well-bound mtDNA fraction (no cross-linking treatment) in four replicate studies. Free proteins, which are not bound to mtDNA, moved out from the well plug (see Supplemental Figure 4B online). A database search for protein identification was performed with MASCOT software against the UniProKB/Swiss-Prot database for Viridiplantae (green plants, 28,773 protein entries). Matched proteins were filtered with a significant threshold (P value) of <0.009 (see Methods).

a

The protein score from a MASCOT MS/MS search derived from the matched peptide ion scores.

b

The Exponetially Modified Protein Abundance Index (emPAI), a program integrated in the MASCOT search engine to quantify the relative amount of protein in a mixture based on protein coverage by the peptide matches.

c

The protein sequence coverage derived from the matched peptides for the protein.

d

The MASCOT MS/MS ion score for the matched peptide.