Table 1.

S-nitrosylation sites identified via SNO-RAC proteomic analysis for proteins that were previously determined to be S-nitrosylated with 2D DyLight Fluor DIGE

Protein Name	Protein ID	Peptide Sequence	SNO Cys	Ion Score	SNO Ratio
α-Enolase	P17182	FGANAILGVSLAVCK	119	91
		SCNCLLLK	337, 339	57
		SGETEDTFIADLVVGLCTGQIK	379	129
Aconitate hydratase	Q99KI0	VAVPSTIHCDHLIEAQVGGEK	126	65
		GGTGAIVEYHGPGVDSISCTGMATICNMGAEIGATTSVFPYNHR	277, 284	107
		VGLIGSCTNSSYEDMGR	385	117	74.7*
		CKSQFTITPGSEQIR	410	86
		DVGGIVLANACGPCIGQWDR	448, 451	97	844.0*
		CTTDHISAAGPWLK	592	89	543.5*
Acyl-CoA dehydrogenase	P45952	MTEQPMMCAYCVTEPSAGSDVAAIK	157, 159	105
		ELNMGQRCSDTR	244	25
ATP synthase-α	Q03265	LYCIYVAIGQK	244	78	336.1*
		YTIVVSATASDAAPLQYLAPYSGCSMGEYFR	294	63
Creatine kinase, M-type	P07310	GYTLPPHCSR	146	47	639.9*
		FCVGLQK	254	35	111.9*
		AGHPFMWNEHLGYVLTCPSNLGTGLR	283	63
Electron transfer flavoprotein subunit-α	Q99LC5	LGGEVSCLVAGTK	53	85	71.5*
		CDKVVQDLCK	60, 68	47
		QFSYTHICAGASAFGK	109	102
		TIYAGNALCTVK	155	92	61.0*
Electron transfer flavoprotein subunit-β	Q9DCW4	HSMNPFCEIAVEEAVR	42	99
		EIIAVSCGPSQCQETIR	66, 71	96	109.2*
		QAIDDDCNQTGQMTAGLLDWPQGTFASQVTLEGDK	131	61
Heat shock protein 60 kDa	P63038	CEFQDAYVLLSEK	237	78
		AAVEEGIVLGGGCALLR	442	98
		CIPALDSLKPANEDQK	447	79
Heat shock protein 70 kDa	P63017	VCNPIITK	503	49
Malate dehydrogenase, cytoplasmic	P14152	VIVVGNPANTNCLTASK	137	97	149.5*
		ENFSCLTR	151	48	160.4*
Malate dehydrogenase, mitochondrial	P08249	GYLGPEQLPDCLK	89	89	154.4*
		GCDVVVIPAGVPR	93	69	178.4*
		TIIPLISQCTPK	212	71	94.6*
		EGVVECSFVQSK	275	75	133.9*
		ETECTYFSTPLLLGK	285	86	336.5*
Myoglobin	P04247	HGCTVLTALGTILK	67	90	1,000*
Myosin light chain 3	P09542	ITYGQCGDVLR	85	74	48.1*
		LMAGQEDSNGCINYEAFVK	191	120	153.7*
NADH-ubiquinone oxidoreductase, 75-kDa subunit	Q91VD9	FCYHER	64	31
		VVAACAMPVMK	92	61	35.6*
		VDSDNLCTEEIFPTEGAGTDLR	367	90
		HSFCEVLK	463	53
		MLFLLGADGGCITR	554	100
		DCFIVYQGHHGDVGAPMADVILPGAAYTEK	564	69
		AVTEGAQAVEEPSIC	727	52	62.3*

Peptides were filtered at a false discovery rate of 1%; peptides with ion scores < 25 were not accepted.

M, mitochondrial isoform; C, S-nitrosylation (SNO) cysteine residue; c, N-ethylmaleimide (NEM)-blocked cysteine residue.

Peptide quantitative ratio (SNO ratio) was determined via label-free peptide analysis; ratio maximum was capped at 1,000.

^*Peptides detected in S-nitrosoglutathione (GSNO)-treated and nontreated samples, P < 0.05 vs. non-GSNO-treated. Peptides not detected under perfusion conditions contain a blank space in the ratio column.

SNO-RAC, SNO-resin-assisted capture; 2D DyLight Fluor DIGE, two-dimensional fluorescence difference gel electrophoresis with DyLight maleimide; CoA, coenzyme A.