Table 5.

Example of iTRAQ measurements for proteins that are known to carry possible phosphorylation at the indicated Ser and Tyr sites (note “S” and “Y” in bold).

Protein/peptide	MH+	ΔM	z	-10lg(p)	Xcorr	ΔCn	RSp	Normalized iTRAQ
								116/114	117/114
Q15365|PCBP1_HUMAN Poly(rC)-binding protein 1 (Alpha-CP1) (hnRNP-E1)
R.L]LMHGK*EVGSIIGK*.K	1914.2	1.9	3	70	4.52	0.35	1
R.L]LMHGK*EVGSIIGK*.K	1914.2	1.1	3	71	4.53	0.38	1	0.87	0.73
R.L]LMHGK*EVGSIIGK*.K	1914.2	0.3	3	71	4.01	0.30	1
R.L]LMHGK*EVGSIIGK*.K	1914.2	1.2	3	66	4.14	0.38	1
R.Q]QSHFAMMHGGTGFAGIDSSSPEVK*.G	2894.4	1.1	3	115	5.90	0.41	1	1.33	1.96
R.Q]QSHFAMMHGGTGFAGIDSSSPEVK*.G	2894.4	1.1	3	87	4.85	0.43	1	3.66	2.87
R.Q]QSHFAMMHGGTGFAGIDSSSPEVK*.G	2894.4	1.1	3	109	5.26	0.45	1	3.44	3.81
R.Q]QSHFAMMHGGTGFAGIDSSSPEVK*.G	2894.4	1.1	3	57	4.32	0.43	1	1.77	2.03
O95817|BAG3_HUMAN BAG family molecular chaperone regulator 3 (BCL-2-binding athanogene-3)
R.S]SLGSHQLPR.G	1225.7	0.1	2	21	2.62	0.22	43
K.T]HYPAQQGEYQTHQPVYHK*.I	2600.3	1.0	3	67	3.69	0.29	1	4.21	2.06
K.T]HYPAQQGEYQTHQPVYHK*.I	2600.3	0.1	3	32	4.08	0.33	1
K.T]HYPAQQGEYQTHQPVYHK*.I	2600.3	1.0	3	36	3.97	0.20	1	3.39	2.76
K.T]HYPAQQGEYQTHQPVYHK*.I	2600.3	1.1	3	29	3.74	0.39	1	1.73	2.04
K.T]HYPAQQGEYQTHQPVYHK*.I	2600.3	1.0	3	47	3.88	0.36	1
R.EGHPVYPQLRPGYIPIPVLHEGAENR.Q	3082.6	1.4	3	51	3.90	0.17	4	1.97	2.72
R.GYISIPVIHEQNVTRPAAQPSFHQAQK.T	3304.8	1.3	3	57	3.03	0.20	3

Note 1: Marks “]” and “*” indicate the iTRAQ tag at the Nt and Lys residues, respectively. S/Y in bold indicate known p-sites.

Note 2: MH+ - molecular weight of protonated molecular ion; ΔM - difference between the theoretical and experimental mass of the protonated molecular ion; p-value - probability of a random match; Xcorr - cross-correlation score between virtual and experimental spectrum; ΔCn - degree by which the lower ranked peptide scores differ from the correlation score of the best match; RSp - rank of preliminary score.

Note 3: Blank iTRAQ ratio cells represent peptides for which iTRAQ ratios were not generated by the LTQ.