Table 3B.

Gel Spots Differentially Phosphorylated after Spinal Cord Injury

Gel spot number and associated protein isoformsa	Vol. Ratio SCI	Vol. Ratio sham	Fold change	NCBI acces. no.	Seq. cov. (%)b	No. of peptides	Theoretical MW/pIe	Functions
29. Glyceraldehyde-3-phosphate dehydrogenase	↑ 1.23 ± 0.34**	0.56 ± 0.16	2.20	P04797‡	54	33/–	36/8.4	Glycolytic enzyme
34. Ubiquitin carboxyl-terminal hydrolase isozyme L1	↑ 1.50 ± 0.66**	0.24 ± 0.14	6.25	Q9R0P9‡	71	36/–	25/5.1	Deubiquitinating enzyme
27. Cathepsin D precursor	↓ 3.23 ± 1.24*	7.41 ± 3.30	−2.29	P24268¶	6	–/2	45/6.7	Aspartyl protease
28. Neurofilament light chain	↓ 2.74 ± 0.81*	6.77 ± 3.80	−2.47	P19527†¶	20	11/1	61/4.6	Axonal cytoskeleton

The volume ratio (Vol. Ratio) of the Pro-Q Diamond and SYPRO Ruby signals (calculated from Vol_Pro-Q/Vol_{SYPRO Ruby}) was used to quantify the relative phosphorylation level of each gel spot; Mean Fold Change was calculated from the ratio of SCI/sham; fold decreases were calculated by dividing 1 by the ratio of the injured to sham samples; ^arefers to the spot numbers in Figure 1; ^brefers to the total percentage of the sequence covered by peptide mass fingerprinting (PMF); ^crefers to the number of peptides that match the sequence for PMF; ^drefers to the number of peptides used to identify a protein by tandem mass spectrometry (MS/MS) (CI% > 95%); ^erefers to the theoretical molecular weight (MW) and the theoretical isoelectric point (pI); ^*p < 0.05; ^**p < 0.01; †Protein Score CI% >95%, ‡Protein Score CI% > 99%; ¶Total Ion Score CI% >99%.