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. 2009 Jun;8(6):1265–1277. doi: 10.1074/mcp.M800377-MCP200

Table III.

LC-MS/MS analysis of the proteins released from Ca2+-treated mitochondria

Protein species present in bands C1–14 (supernatant of Ca2+-treated mitochondria) were determined by LC-MS/MS analysis. Those present in the gel pieces in lane A (supernatant of non-treated mitochondria) corresponding to the positions of bands C1–14 were also determined as backgrounds and are shown in the column designated as “Non-treated.” AC, UniProt accession number; PH, pleckstrin homology.

Band no. in lane C Identified protein
Number of detected peptidesc (%)d
Name AC Molecular massa Locb Non-treated Ca2+-treated
1 Carbamoyl-phosphate synthase P07756 166 M 31 (65) 61 (94)
Aspartate aminotransferase P00507 48 M 7 (15) 0 (0)
Catalase P04762 60 Pr 4 (8) 1 (2)
Aldehyde dehydrogenase P11884 57 M 2 (4) 0 (0)
Hydroxymethylglutaryl-CoA synthase P22791 57 Mt 2 (4) 1 (2)
Malate dehydrogenase P04636 36 M 0 (0) 1 (2)
Thiosulfate sulfurtransferase P24329 33 M 2 (4) 0 (0)
2 Carbamoyl-phosphate synthase P07756 166 M 50 (84) 58 (93)
Pyruvate carboxylase P52873 130 M 5 (8) 0 (0)
Bile acid CoA:amino acid N-acyltransferase Q63276 47 Pr 3 (5) 1 (2)
Catalase P04762 60 Pr 2 (3) 3 (5)
3 Carbamoyl-phosphate synthase P07756 166 M 18 (60) 22 (42)
Dimethylglycine dehydrogenase Q63342 96 Mt 6 (20) 14 (26)
Aspartate aminotransferase P00507 48 M 4 (13) 1 (2)
Aconitate hydratase Q9ER34 86 Mt 2 (7) 16 (30)
4 Sulfite oxidase Q07116 55 IMS 18 (38) 11 (69)
Dihydrolipoyl dehydrogenase Q63342 55 M 12 (25) 2 (13)
Glutamate dehydrogenase 1 P10860 62 M 10 (21) 0 (0)
Carbamoyl-phosphate synthase P07756 166 M 8 (17) 1 (6)
Hydroxymethylglutaryl-CoA synthase P22791 57 M 0 (0) 1 (6)
Methylmalonate-semialdehyde dehydrogenase Q02253 58 M 0 (0) 1 (6)
5 Hydroxymethylglutaryl-CoA synthase P22791 57 M 24 (58) 18 (100)
Carbamoyl-phosphate synthase P07756 166 M 6 (15) 0 (0)
Fumarate hydratase P14408 55 Mt 5 (12) 0 (0)
Acyl-coenzyme A oxidase 1 P07872 75 Pr 4 (10) 0 (0)
Retinoid-inducible serine carboxypeptidase Q920A6 51 S 2 (5) 0 (0)
6 Long chain-specific acyl-CoA dehydrogenase P15650 48 M 23 (37) 11 (35)
3-Ketoacyl-CoA thiolase P13437 42 Mt 16 (25) 12 (39)
Acetyl-CoA acetyltransferase P17764 45 Mt 7 (11) 1 (3)
Aspartate aminotransferase P00507 48 M 5 (8) 5 (17)
Medium chain-specific acyl-CoA dehydrogenase P08503 47 M 5 (8) 1 (3)
Cathepsin D P24268 45 Ly 4 (6) 1 (3)
Fumarylacetoacetase P25093 46 ? 3 (5) 0 (0)
7 Aspartate aminotransferase P00507 48 M 32 (51) 37 (86)
3-Ketoacyl-CoA thiolase A P13437 44 Pr 11 (17) 0 (0)
Short chain-specific acyl-CoA dehydrogenase P15651 45 M 10 (16) 3 (7)
α-Methylacyl-CoA racemase P70473 42 Pr, Mt 6 (10) 3 (7)
Cathepsin D P24268 45 Ly 2 (3) 0 (0)
PH domain leucine-rich repeat protein phosphatase Q9WTR8 186 Cy 1 (2) 0 (0)
Thiosulfate sulfurtransferase P24329 33 M 1 (2) 0 (0)
8 Ornithine carbamoyltransferase P00481 40 M 21 (50) 23 (64)
Thiosulfate sulfurtransferase P24329 33 M 13 (31) 13 (36)
Arginase-1 P07824 35 Cy 4 (10) 0 (0)
Carbamoyl-phosphate synthase P07756 166 M 3 (7) 0 (0)
Malate dehydrogenase P04636 36 M 3 (7) 0 (0)
Glyceraldehyde-3-phosphate dehydrogenase P04797 36 Cy 1 (2) 0 (0)
9 Malate dehydrogenase P04636 36 M 22 (58) 34 (76)
Hydroxyacyl-CoA dehydrogenase P22791 35 M 8 (21) 5 (11)
l-Lactate dehydrogenase A chain P04642 37 Cy 4 (11) 0 (0)
Thiosulfate sulfurtransferase P24329 33 M 3 (8) 0 (0)
Cathepsin Z NP_899159e 35 Ly 1 (3) 1 (2)
Peroxisomal trans-2-enoyl-CoA reductase Q9WVK3 33 Pr 0 (0) 3 (7)
10 Hydroxyacyl-Co A dehydrogenase P22791 35 M 16 (52) 9 (40)
Electron transfer flavoprotein subunit α P13803 35 M 9 (29) 4 (17)
Malate dehydrogenase P04636 36 M 2 (6) 0 (0)
3-Mercaptopyruvate sulfurtransferase P97532 33 Cy, Mt 2 (6) 1 (4)
Cathepsin Z NP_899159e 35 Ly 1 (3) 1 (4)
Thiosulfate sulfurtransferase P24329 33 M 1 (3) 0 (0)
Peroxisomal trans-2-enoyl-CoA reductase Q9WVK3 33 Pr 0 (0) 4 (17)
Hydroxymethylglutaryl-CoA synthase P22791 57 M 0 (0) 2 (9)
Hydroxymethylglutaryl-CoA lyase P97519 35 M 0 (0) 1 (4)
11 Electron transfer flavoprotein subunit aα P13803 35 M 15 (26) 20 (40)
3-Mercaptopyruvate sulfurtransferase P97532 33 Cy, Mt 11 (19) 10 (20)
Hydroxyacyl-Co A dehydrogenase P22791 35 M 9 (16) 3 (6)
2,4-Dienoyl-CoA reductase Q64591 36 Mt 7 (12) 7 (14)
Δ3,5-Δ2,4-Dienoyl-CoA isomerase Q62651 36 Mt, Cy 5 (9) 1 (2)
Thiosulfate sulfurtransferase P24329 33 M 5 (9) 2 (4)
Betaine-homocysteine S-methyltransferase O09171 45 Cy 3 (5) 0 (0)
Retinoid-inducible serine carboxypeptidase Q920A6 51 S 2 (3) 0 (0)
Cathepsin Z NP_899159e 35 Ly 1 (2) 0 (0)
3-Hydroxyisobutyrate dehydrogenase P29266 36 Mt 0 (0) 5 (10)
Hydroxymethylglutaryl-CoA synthase P22791 57 M 0 (0) 2 (4)
12 Enoyl-CoA hydratase P14604 32 M 15 (43) 14 (26)
Adenylate kinase isoenzyme 2 P29410 27 IMS 11 (31) 17 (32)
Electron transfer flavoprotein subunit β Q68FU3 28 M 4 (11) 10 (19)
Hydroxymethylglutaryl-CoA synthase P22791 57 M 2 (6) 0 (0)
3,2-trans-Enoyl-CoA isomerase P23965 32 M 3 (9) 11 (21)
Adenylate kinase isoenzyme 4 Q9WUS0 25 M 0 (0) 1 (2)
13 Ribonuclease UK114 P52759 14 Mt, Cy 4 (24) 6 (20)
Cytochrome c P62898 12 IMS 4 (24) 13 (45)
Hemoglobin subunit β -1 P02091 12 Bl 3 (18) 2 (7)
Fatty acid-binding protein, liver P02692 12 Cy 3 (18) 8 (28)
Hemoglobin subunit α P01946 12 Bl 3 (18) 0 (0)
14 10-kDa heat shock protein P26772 11 M 6 (75) 14 (83)
Betaine-homocysteine S-methyltransferase O09171 45 Cy 2 (25) 2 (11)
a

In kDa.

b

Location of the individual proteins is shown by the following abbreviations: Bl, Red blood cell; Cy, cytosol; IMS, intermembrane space; Ly, lysosome; M, matrix; Mt, mitochondria; Pr, peroxisome; ?, unknown.

c

Number of peptides derived from each protein identified by LC-MS/MS analysis.

d

Relative proportions of the peptide number derived from the protein to the total number of the peptides detected in each protein band are shown.

e

NCBI accession number.