Table 1.
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).
The protein score from a MASCOT MS/MS search derived from the matched peptide ion scores.
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.
The protein sequence coverage derived from the matched peptides for the protein.
The MASCOT MS/MS ion score for the matched peptide.