Table 3. Description of differentially expressed proteins found in this study.

Proteins were considered differentially modulated at statistically significant difference in normalized volume in each comparison between the treatments (GM; non-GM; GM D; non-GM D; GM DH) at ANOVA P < 0.05 according to Table 2. Proteins were classified in functional categories based on the KEGG Orthology databases and on careful literature evaluation. The table reports spot number (Match ID), accession number and protein name, together with Mascot score, sequence coverage, number of matched peptides, theoretical and experimental molecular weight (MW) and isoelectric point (pI).

Spot ID	Accession	Protein Name	Mascot Score	Sequence Coverage (%)	Peptides	Theor. Mass (kDa)	Theor. pI (pH)	Exp. Mass (kDa)	Exp. pI (pH)	Biological Process / Molecular Function
1689	NP_001150872	ATP synthase subunit gamma, chloroplastic precursor (Zea mays)	520	31	12	54	5.31	52	5.4	Energy metabolism / Stress response (ATP synthesis coupled proton transport)
1576	ACG33858	Ferredoxin-NADP reductase, (Zea mays)	536	44	19	40	8.56	44	8.2	Energy metabolism (oxidoreductase; nucleotide binding)
1364	ACG25364	Photosystem I reaction center subunit II (Zea mays)	220	24	5	21	9.77	20	9.1	Energy metabolism (photosynthesis)
1329	NP_001149700	Photosystem I reaction center subunit IV A (Zea mays)	204	47	6	14	9.79	15	9.1	Energy metabolism (photosynthesis)
1881	YP_024377	ATP synthase CF1 alpha subunit (Saccharum hybrid cultivar SP-80-3280)	842	40	17	55	5.87	55	5.8	Energy metabolism (ATP hydrolysis-coupled proton transport)
1826	NP_043032	ATP synthase CF1 beta subunit (chloroplast) (Zea mays)	237	16	5	54	5.31	55	5.4	Energy metabolism (ATP hydrolysis-coupled proton transport)
1511	ACG31416	NAD-dependent epimerase/dehydratase (Zea mays)	264	35	7	31	9.11	30	9.1	Carbohydrate metabolism (catalytic activity)
1261	NP_039445	Photosystem I subunit VII (chloroplast) (Zea mays)	110	46	3	8	6.51	8	6.2	Energy metabolism (photosynthetic electron transport in photosystem I; oxidoreductase)
1429	XP_008652004	Oxygen-evolving enhancer protein 2, chloroplastic (Zea mays)	345	37	8	31	9.50	33	9.1	Energy metabolism (photosynthesis; calcium ion binding; photosystem I)
1756	NP_001147628	Phosphoglycerate kinase (Zea mays)	413	23	10	50	6.07	48	5.8	Carbohydrate metabolism (glycolytic process; phosphorylation)
1365	ACG28186	Cytochrome b6-f complex iron-sulfur subunit (Zea mays)	204	28	5	24	8.52	21	8.4	Energy metabolism (photosynthesis; oxidoreductase activity; electron transport)
1529	ACG27183	Inorganic pyrophosphatase (Zea mays)	744	49	19	31	5.79	30	5.9	Carbohydrate metabolism (phosphate-containing compound metabolic process; magnesium ion binding)
1341	XP_008654301	psbP-like protein 2, chloroplastic (Zea mays)	301	36	8	25	8.34	25	7.5	Energy metabolism (photosynthesis; calcium ion binding; photosystem II)
1763	AAL67577	3-phosphoshikimate-1-carboxyvinyltransferase (Glycine max)	944	50	19	47	5.13	49	5.2	Energy metabolism (chorismate biosynthetic process; shikimate pathway);
1743	NP_001104921	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic precursor (Zea mays)	487	31	12	47	6.29	49	6.4	Energy metabolism (Calvin cycle; ATP binding; activation of RuBisCO)
1848	NP_043033	Ribulose bisphosphate carboxylase large subunit (Zea mays)	521	27	12	52	6.33	52	6.3	Energy metabolism (photosynthesis; carbon fixation)
1449	4RTH_A	Chain A, The Crystal Structure of Psbp (Zea mays)	272	44	6	20	5.96	21	6.0	Energy metabolism (photosynthesis; calcium ion binding)
1638	NP_001142100	Malate dehydrogenase (Zea mays)	110	22	4	35	8.23	34	8.2	Carbohydrate metabolism (oxidoreductase)
1617	ACG33017	Fructose-bisphosphate aldolase (Zea mays)	522	27	10	40	5.39	39	6.1	Carbohydrate metabolism (glycolysis; carbohydrate degradation)
1581	NP_001141303	Uncharacterized protein LOC100273394 (Zea mays)	109	11	3	31	5.57	31	5.4	Unidentified