. Author manuscript; available in PMC: 2011 Nov 5.

Published in final edited form as: J Proteome Res. 2010 Oct 12;9(11):5705–5714. doi: 10.1021/pr1005179

Table 2.

List of proteins and peptides bearing PB-DOPA identified in HeLa cell mitochondrial fraction

No	Proteins	IPI#	Sequences ^a	Stochiometry ^b
No	Proteins	IPI#	Sequences ^a	Spectra # (Modified/Unmodified	%
1	Annexin A2 isoform 1	IPI00418169	TPAQYDASELK	1/42	2.4

2	Electron transfer flavoprotein subunit alpha	IPI00010810	VLVAQHDVYK^*	1/9	10.0

3	Inosine-5′-monophosphate dehydrogenase 2	IPI00291510	VSEYAR^*	1/7	12.5

4	Glyceraldehyde-3-phosphate dehydrogenase	IPI00219018	YDDIKK	5/71	6.6
4	Glyceraldehyde-3-phosphate dehydrogenase	IPI00219018	YDNSLK^*	2/12	14.3

5	Protein disulfide-isomerase A3	IPI00025252	YKELGEK	3/44	6.4
5	Protein disulfide-isomerase A3	IPI00025252	LAPEYEAAATR	1/55	1.8

6	Catalase	IPI00465436	LFAYPDTHR	5/62	7.5

7	Superoxide dismutase 2, mitochondrial	IPI00022314	HHAAYVNNLNVTEEK^*	2/19	9.5

Hydroxylation sites are denoted in bold and underline.

PTM stoichiometry (%) is the ratio of the number of MS/MS spectra for the peptide bearing the PB-DOPA residue divided by the number of MS/MS spectra for the both peptides bearing the corresponding Tyr site, namely the unmodified peptides with or without missing cleavages (cutoff PTMap score > 0.5, FDR < 1%) and modified peptides (cutoff PTMap score > 1.0, FDR < 5%).

denote PB-DOPA peptides with high stoichiometry (≥10%).