. 2010 May 13;9(9):1937–1953. doi: 10.1074/mcp.M900483-MCP200

Table I. Comparison of protein abundance changes determined by iTRAQ labeling of nuclear fractions from IL-4-treated anti-CD3/CD28-activated CD4⁺ cells versus anti-CD3/CD28-activated CD4⁺ cells at 6 and 24 h with LC-MS/MS analysis.

The iTRAQ ratios (Th2/Th0) are relative to the protein abundance of the activated cells (without IL-4) at the equivalent time points. The values are, unless otherwise stated, based on the weighted average from three biological replicates. These values were estimated using a random effect model. The inclusion criteria for these proteins are based on an absolutes Z score greater than 1.96 (p < 0.05), an abundance change greater than 20% (up or down), detection of the proteins in all three iTRAQ experiments, two or more associated peptides, and five or more iTRAQ ratios. Some exceptions are marked. The p values were calculated from the normal distribution of the absolute value of the Z score. PQ seq., number of unique peptides detected by ProQuant; Tot. calcs., total number of calculations used; Cov., coverage; NA, not applicable.

Accession	Name	GO location	iTRAQ 6-h ratio	+/−	6-h p value	6-h FDR	iTRAQ 24-h ratio	+/−	24-h p value	FDR	PQ seq.	Tot. calcs.	Cov.
													%
Th2 association
STAT6_HUMAN (P42226)	Signal transducer and activator of transcription 6	Nucleus, cytoplasm	1.32	0.12	0.001	0.02	1.07	0.15	0.60	0.86	3	10	5
SATB1_HUMAN (Q01826)	DNA-binding protein SATB1	Nucleus	1.12	0.03	3·e−05	9·e−04	1.24	0.08	0.001	0.018	11	47	14
IKZF1_HUMAN^a (Q13422)	DNA-binding protein Ikaros	Intracellular, nucleus	1.04	0.03	0.15	0.56	1.21	0.11	0.046	0.25	5	31	18
Interferon-related
TRI22_HUMAN (Q8IYM9)	Tripartite motif-containing protein 22	Intracellular, nucleus	0.82	0.08	0.055	0.32	0.81	0.07	0.018	0.143	3	9	9
STAT1_HUMAN^b (P42224)	Signal transducer and activator of transcription 1-α/β	Cytoplasm, nucleus	0.95	0.06	0.39	0.81	0.81	0.12	0.16	0.51	8	19	5
IF16_HUMAN^a,b (Q16666)	g-Interferon-inducible protein IFI16	Nucleus, cellular component	0.99	0.02	0.75	0.95	0.85	0.04	0.001	0.012	22	142	39
TBX21_HUMAN^c (Q9UL17)	T box transcription factor TBX21	Nucleus	0.98	0.09	0.83	NA	0.64	0.11	0.01	NA	2	5	4
TCF7_HUMAN^d (P36402)	Transcription factor 7 (T cell-specific transcription factor 1)	Cytoplasm, membrane, nucleus	0.95	0.04	0.17	0.60	0.75	0.03	2·e−08	2·e−6	2	13	8
Other
YBOX1_HUMAN (P67809)	Nuclease-sensitive element-binding protein 1 (Y box-binding protein 1)	Nucleus	1.23	0.10	0.11	0.50	1.65	0.30	0.006	0.069	4	18	30
G10_HUMAN^a (P41223)	Protein BUD31 homolog (protein G10 homolog) (EDG-2)	Nucleus	0.97	0.05	0.68	0.92	1.24	0.05	7·e−08	5·e−06	3	10	26
AKAP8_HUMAN (O43823)	Protein kinase A anchor protein 8	Intracellular, membrane, nucleus, chromosome	1.10	0.06	0.26	0.70	1.24	0.13	0.045	0.25	3	9	6
RPB1_HUMAN^a (P24928)	DNA-directed RNA polymerase II largest subunit	Nucleus, cellular component	1.45	0.17	0.046	0.29	0.86	0.33	0.70	0.90	2	5	3
TAF10_HUMAN (Q12962)	Transcription initiation factor TFIID subunit 10	Nucleus, cytoplasm, cellular component	1.59	0.14	0.002	0.03	0.90	0.06	0.095	0.42	2	14	2
RL5_HUMAN^a (P46777)	60 S ribosomal protein L5	Intracellular, nucleus	1.36	0.13	0.042	0.27	1.66	0.35	0.016	0.13	6	23	27
RFC1_HUMAN^a (P35251)	Replication factor C subunit 1	Nucleus, chromosome	1.01	0.03	0.75	0.94	1.24	0.13	0.038	0.23	7	17	10
MP2K3_HUMAN^e (P46734)	Dual specificity mitogen-activated protein kinase kinase 3		1.82	0.08	1·e−15	0.00	0.92	0.04	0.086	0.38	1	11	9
CD3E_HUMAN^a (P07766)	T cell surface glycoprotein CD3 ϵ chain precursor	Cell surface, membrane	1.25	0.10	0.004	0.05	1.16	0.07	0.016	0.132	2	10	14
CD5_HUMAN (P06127)	T cell surface glycoprotein CD5 precursor	Cell surface, membrane	0.90	0.07	0.142	0.55	0.73	0.07	0.001	0.015	3	9	15
CD45_HUMAN^a (P08575)	Leukocyte common antigen precursor	Membrane	0.99	0.05	0.864	0.97	0.80	0.09	0.043	0.244	6	33	6
CD44_HUMAN (P16070)	CD44 antigen precursor	Cell surface, membrane	0.91	0.04	0.032	0.23	0.77	0.09	0.027	0.191	6	46	10
GLU2B_HUMAN^a (P14314)	Glucosidase 2 subunit β precursor	Membrane	1.23	0.04	1·e−08	0.00	1.07	0.02	2·e−05	0.001	3	8	6
PSB8_HUMAN (P28062)	Proteasome subunit β type 8 precursor	Intracellular	1.03	0.06	0.670	0.92	0.83	0.03	2·e−06	7·e−05	1	8
PSME3_HUMAN (P61289)	Proteasome activator complex subunit 3	Intracellular	0.93	0.07	0.341	0.79	0.73	0.05	6·e−07	3·e−05	4	10	19
GNAS_HUMAN (P63092)	Guanine nucleotide-binding protein G_s subunit α isoforms, short	Intracellular	0.72	0.08	0.004	0.05	1.14	0.39	0.688	0.900	2	10	14
ATP5J_HUMAN (P18859)	ATP synthase coupling factor 6, mitochondrial precursor	Cytoplasm	1.23	0.12	0.032	0.23	0.74	0.15	0.126	0.464	2	12	22
GRAP2_HUMAN (O75791)	GRB2-related adapter protein 2	Cytoplasm	1.00	0.01	0.816	0.96	1.27	0.08	6·e−05	0.002	6	18	12
APT_HUMAN^a (P07741)	Adenine phosphoribosyl- transferase	Cytoplasm	0.99	0.02	0.723	0.93	0.83	0.08	0.045	0.243	4	24	25
HS105_HUMAN^a (Q92598)	Heat-shock protein, 105 kDa	Cytoplasm	1.24	0.07	4·e−04	0.01	1.09	0.12	0.436	0.755	4	12	6
TXLNA_HUMAN^a (P40222)	α-Taxilin	Cytoplasm, extracellular region	1.38	0.14	0.001	0.02	1.01	0.07	0.848	0.967	3	9	13
S10A9_HUMAN^a (P06702)	Protein S100-A9 (S100 calcium-binding protein A9)	Extracellular space	1.27	0.09	4·e−04	0.01	1.82	1.09	0.289	0.653	4	7	31

^a Detected in the published T cell nucleus data sets of Han and co-workers (34, 35).

^b Included but did not pass inclusion criteria.

^c In one biological replicate only.

^d Shared peptides with LEF1 (Q9UJU2) and TF7L2 (Q9NQB0) support this change.

^e Mascot provided two additional sequences.

Table I. Comparison of protein abundance changes determined by iTRAQ labeling of nuclear fractions from IL-4-treated anti-CD3/CD28-activated CD4+ cells versus anti-CD3/CD28-activated CD4+ cells at 6 and 24 h with LC-MS/MS analysis.

Table I. Comparison of protein abundance changes determined by iTRAQ labeling of nuclear fractions from IL-4-treated anti-CD3/CD28-activated CD4⁺ cells versus anti-CD3/CD28-activated CD4⁺ cells at 6 and 24 h with LC-MS/MS analysis.