Table II.

Proteins preferentially accumulated in stele tissue of maize primary roots compared with cortex identified after 2-DE separation and nano-HPLC-ESI-MS/MS analysis of trypsin-digested proteins matched against the NCBI.nr protein database entries

Preferentially accumulated proteins, >2-fold change; t test, P < 0.01 in three independent biological replicates.

Spot No.	Stele Specificitya	MOWSE Scoreb	Sequence Coveragec	Mr Predicted/Mr Geld	pI Predicted/pI Gele	Function NCBI.nr [Species] Accession No.f	t Test Pg	FDR Ph
Metabolism
60	3.2	1705	33	92.9/93.8	6.0/6.6	Sucrose synthase 1 [Z. mays] NP_001105323	<0.001	0.007
61	2.5	828	17	83.7/86.0	5.9/6.2	Methionine synthase protein [Sorghum bicolor] AAL73979	<0.001	0.003
62	2.3	675	22	52.9/56.3	6.1/5.8	UDP-Glc dehydrogenase [Colocasia esculenta] AAO62313	0.004	0.029
Disease/defense/stress response
63	Stele only	636	19	57.2/60.8	5.6/5.8	TCP-1/cpn60 chaperonin family protein [O. sativa] NP_001050672i	<0.001	0.010
64	Stele only	881	20	59.0/67.9	5.4/5.7	T-complex protein 1 subunit ε (TCP-1/cpn60 chaperonin family) [Avena sativa] P54411	<0.001	0.002
65	3.4	183	14	22.4/29.4	5.5/5.6	Remorin 1 [O. sativa] NP_001053409i	0.004	0.030
66	2.4	111	8	35.9/41.7	5.8/6.6	Peroxidase [O. sativa] NP_001058379i	<0.001	0.006
67	2.1	379	10	62.0/76.3	5.3/5.4	Peptidyl-prolyl isomerase [O. sativa] Q43207	<0.001	0.039
Energy
68	Stele only	162	9	19.8/17.9	5.3/5.1	ATP synthase D chain [Solanum demissum] AAT40531	0.004	0.031
Cell fate
69	2.4	246	19	41.7/44.8	5.2/5.1	Actin [Saccharum officinarum] AAU93346	<0.001	0.049
70	4.3	94	8	41.6/14.5	5.2/5.7	Actin3 [Glycine max] P02580	0.001	0.013

^aRatio of accumulation (fold change) of a particular protein between primary root stele versus cortex tissue.

^bProbability-based MOWSE score is defined as –10 × log(P), where P is the probability that the observed match is a random event. Scores > 43 indicate identity or extensive homology (P < 0.05). Protein scores are derived from ion scores as a nonprobabilistic basis for ranking protein hits.

^cPercentage of predicted protein sequence covered by matched peptides.

^dTheoretical molecular mass of predicted protein/experimental molecular mass of protein on the gel.

^eTheoretical pI of predicted protein/experimental pI of protein on the gel.

^fFunction of sequenced peptides obtained via automated algorithm of the MASCOT software (www.matrixscience.com) from the NCBI.nr database.

^gP values obtained via Student's t test after comparing protein accumulation of three biological replicates of primary root stele versus cortex tissue (cutoff, P ≤ 0.01).

^hP values of the linear contrasts were adjusted according to Wald tests (cutoff, P ≤ 0.05).

ⁱFor protein accessions identified by MASCOT that had no functional annotation, a function was assigned via BLASTP searches of the corresponding protein accession numbers (cutoff, E ≤ 1e⁻¹⁰).