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 CIdentified proteinNumber of detected peptidesc (%)d
NameACMolecular massaLocbNon-treatedCa2+-treated
1Carbamoyl-phosphate synthaseP07756166M31 (65)61 (94)
Aspartate aminotransferaseP0050748M7 (15)0 (0)
CatalaseP0476260Pr4 (8)1 (2)
Aldehyde dehydrogenaseP1188457M2 (4)0 (0)
Hydroxymethylglutaryl-CoA synthaseP2279157Mt2 (4)1 (2)
Malate dehydrogenaseP0463636M0 (0)1 (2)
Thiosulfate sulfurtransferaseP2432933M2 (4)0 (0)
2Carbamoyl-phosphate synthaseP07756166M50 (84)58 (93)
Pyruvate carboxylaseP52873130M5 (8)0 (0)
Bile acid CoA:amino acid N-acyltransferaseQ6327647Pr3 (5)1 (2)
CatalaseP0476260Pr2 (3)3 (5)
3Carbamoyl-phosphate synthaseP07756166M18 (60)22 (42)
Dimethylglycine dehydrogenaseQ6334296Mt6 (20)14 (26)
Aspartate aminotransferaseP0050748M4 (13)1 (2)
Aconitate hydrataseQ9ER3486Mt2 (7)16 (30)
4Sulfite oxidaseQ0711655IMS18 (38)11 (69)
Dihydrolipoyl dehydrogenaseQ6334255M12 (25)2 (13)
Glutamate dehydrogenase 1P1086062M10 (21)0 (0)
Carbamoyl-phosphate synthaseP07756166M8 (17)1 (6)
Hydroxymethylglutaryl-CoA synthaseP2279157M0 (0)1 (6)
Methylmalonate-semialdehyde dehydrogenaseQ0225358M0 (0)1 (6)
5Hydroxymethylglutaryl-CoA synthaseP2279157M24 (58)18 (100)
Carbamoyl-phosphate synthaseP07756166M6 (15)0 (0)
Fumarate hydrataseP1440855Mt5 (12)0 (0)
Acyl-coenzyme A oxidase 1P0787275Pr4 (10)0 (0)
Retinoid-inducible serine carboxypeptidaseQ920A651S2 (5)0 (0)
6Long chain-specific acyl-CoA dehydrogenaseP1565048M23 (37)11 (35)
3-Ketoacyl-CoA thiolaseP1343742Mt16 (25)12 (39)
Acetyl-CoA acetyltransferaseP1776445Mt7 (11)1 (3)
Aspartate aminotransferaseP0050748M5 (8)5 (17)
Medium chain-specific acyl-CoA dehydrogenaseP0850347M5 (8)1 (3)
Cathepsin DP2426845Ly4 (6)1 (3)
FumarylacetoacetaseP2509346?3 (5)0 (0)
7Aspartate aminotransferaseP0050748M32 (51)37 (86)
3-Ketoacyl-CoA thiolase AP1343744Pr11 (17)0 (0)
Short chain-specific acyl-CoA dehydrogenaseP1565145M10 (16)3 (7)
α-Methylacyl-CoA racemaseP7047342Pr, Mt6 (10)3 (7)
Cathepsin DP2426845Ly2 (3)0 (0)
PH domain leucine-rich repeat protein phosphataseQ9WTR8186Cy1 (2)0 (0)
Thiosulfate sulfurtransferaseP2432933M1 (2)0 (0)
8Ornithine carbamoyltransferaseP0048140M21 (50)23 (64)
Thiosulfate sulfurtransferaseP2432933M13 (31)13 (36)
Arginase-1P0782435Cy4 (10)0 (0)
Carbamoyl-phosphate synthaseP07756166M3 (7)0 (0)
Malate dehydrogenaseP0463636M3 (7)0 (0)
Glyceraldehyde-3-phosphate dehydrogenaseP0479736Cy1 (2)0 (0)
9Malate dehydrogenaseP0463636M22 (58)34 (76)
Hydroxyacyl-CoA dehydrogenaseP2279135M8 (21)5 (11)
l-Lactate dehydrogenase A chainP0464237Cy4 (11)0 (0)
Thiosulfate sulfurtransferaseP2432933M3 (8)0 (0)
Cathepsin ZNP_899159e35Ly1 (3)1 (2)
Peroxisomal trans-2-enoyl-CoA reductaseQ9WVK333Pr0 (0)3 (7)
10Hydroxyacyl-Co A dehydrogenaseP2279135M16 (52)9 (40)
Electron transfer flavoprotein subunit αP1380335M9 (29)4 (17)
Malate dehydrogenaseP0463636M2 (6)0 (0)
3-Mercaptopyruvate sulfurtransferaseP9753233Cy, Mt2 (6)1 (4)
Cathepsin ZNP_899159e35Ly1 (3)1 (4)
Thiosulfate sulfurtransferaseP2432933M1 (3)0 (0)
Peroxisomal trans-2-enoyl-CoA reductaseQ9WVK333Pr0 (0)4 (17)
Hydroxymethylglutaryl-CoA synthaseP2279157M0 (0)2 (9)
Hydroxymethylglutaryl-CoA lyaseP9751935M0 (0)1 (4)
11Electron transfer flavoprotein subunit aαP1380335M15 (26)20 (40)
3-Mercaptopyruvate sulfurtransferaseP9753233Cy, Mt11 (19)10 (20)
Hydroxyacyl-Co A dehydrogenaseP2279135M9 (16)3 (6)
2,4-Dienoyl-CoA reductaseQ6459136Mt7 (12)7 (14)
Δ3,52,4-Dienoyl-CoA isomeraseQ6265136Mt, Cy5 (9)1 (2)
Thiosulfate sulfurtransferaseP2432933M5 (9)2 (4)
Betaine-homocysteine S-methyltransferaseO0917145Cy3 (5)0 (0)
Retinoid-inducible serine carboxypeptidaseQ920A651S2 (3)0 (0)
Cathepsin ZNP_899159e35Ly1 (2)0 (0)
3-Hydroxyisobutyrate dehydrogenaseP2926636Mt0 (0)5 (10)
Hydroxymethylglutaryl-CoA synthaseP2279157M0 (0)2 (4)
12Enoyl-CoA hydrataseP1460432M15 (43)14 (26)
Adenylate kinase isoenzyme 2P2941027IMS11 (31)17 (32)
Electron transfer flavoprotein subunit βQ68FU328M4 (11)10 (19)
Hydroxymethylglutaryl-CoA synthaseP2279157M2 (6)0 (0)
3,2-trans-Enoyl-CoA isomeraseP2396532M3 (9)11 (21)
Adenylate kinase isoenzyme 4Q9WUS025M0 (0)1 (2)
13Ribonuclease UK114P5275914Mt, Cy4 (24)6 (20)
Cytochrome cP6289812IMS4 (24)13 (45)
Hemoglobin subunit β -1P0209112Bl3 (18)2 (7)
Fatty acid-binding protein, liverP0269212Cy3 (18)8 (28)
Hemoglobin subunit αP0194612Bl3 (18)0 (0)
1410-kDa heat shock proteinP2677211M6 (75)14 (83)
Betaine-homocysteine S-methyltransferaseO0917145Cy2 (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.