Table II

Proteins identified uniquely in skeletal muscle

Matrix protein samples were resolved and identified by GeLC-MS/MS. Upon BLASTing of the muscle sequences against the sequences identified in heart and liver matrix samples, we obtained a list of 21 proteins found only in skeletal muscle (Acc. no., Swiss-Prot or National Center for Biotechnology Information (NCBI) accession code; No. peptides, number of red or bold red peptides used for the identification by Mascot (All top ranking peptides are shown in red in a Mascot report. The first time a peptide match appears in the report it is shown as bold red (Matrix Science).)). If the protein was also identified in an intermembrane space fraction, then “ims” is indicated. The last two columns report the mitochondrial targeting score with Mitopred (only when >60%) and the subcellular localization of the protein if it had an annotation in the Swiss-Prot database (M, mitochondrial; SR, sarcoplasmic reticulum; ER, endoplasmic reticulum; IEA, inferred from electronic annotation). Proteins in bold either have a high prediction score or represent known mitochondrial proteins.

NameAcc. no.No. peptides+ImsMitopredOrganelle
%
47-kDa heat shock protein P29457 2ER
Elongation factor G 2 XP_226707 4 M
AMP deaminase 1, similar to P10759 19
ATP-binding cassette, family F XP_138739 2 92.30
Calmodulin-like 3 P62161 2
Calsequestrin, skeletal muscle isoform P19633 2imsSR
Decorin precursor Q01129 2Secreted
DJ842G6.1.1 XP_215857 2 92.30
Enigma protein, isoform 1 Q9Z1Z9 3imsM (IEA)
Hepatitis C virus core-binding protein 6 XP_341574 2 92.30
Lactotransferrin2Secreted
MGC4767 protein XP_222227 2 100
Mitsugumin 23, similar to XP_342026 2 84.60
Hypothetical protein Q5XIG1 5
Protein CGI-51, similar to XP_217005 11
RIKEN cDNA 1810015H18 XP_215286 2
Sarcoplasmic/ER calcium ATPase 1 Q64578 24ims
Seryl-aminoacyl-tRNA synthetase 2, similar to XP_214884 10 M
Splice isoform DPII of desmoplakin XP_214884 5Desmosomes
TOM22, similar to Q75Q41 2 M
Hypothetical protein (similar to TU12B1-TY) IPI00389238 13