Table 1.

Proteins differentially expressed in cultured S49 and its kin- mutant cells in the presence or absence of a diffusible cAMP analog. Both target-based (PQD/LTQ) and discovery-based (HCD/Orbitrap) acquisitions were conducted with the same tryptic peptides prepared from the lysates. The iTRAQ labeling schemes are described in Materials and Methods. Suppl. Table 1 details the number of peptides and peptide sequences identified.

		Target-based acquisition using PQD			Discovery-based acquisition using HCD
Mutational effect		Ratio115/114	Ratio116/114	Ratio117/114	Ratio115/114	Ratio116/114	Ratio117/114
Glyceraldehyde-3-phosphate dehydrogenase	G3P_MOUSE	1.44	1.18	1.76	1.53	1.15	1.79
Asparagine synthetase [glutamine-hydrolyzing]	ASNS_MOUSE	1.41	0.92	1.30	1.58	0.92	1.58
Staphylococcal nuclease domain-containing protein 1	SND1_MOUSE	1.43	1.00	1.64	1.55	1.00	1.47
Galectin-1	LEG1_MOUSE	3.17	1.42	3.57	2.42	1.31	2.27
Protein disulfide-isomerase A4	PDIA4_MOUSE	1.62	1.01	1.57	1.63	1.01	1.77
Rho GDP-dissociation inhibitor 2	GDIR2_MOUSE	1.70	0.96	1.89	2.02	0.83	1.96
Metallothionein-2	MT2_MOUSE	0.33	0.80	0.41	---	---	---
Serine-threonine kinase receptor-associated protein	STRAP_MOUSE	1.50	0.83	1.43	1.39	0.89	1.17
Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase	MTDC_MOUSE	1.59	1.05	1.74	1.52	0.92	1.39
RuvB-like 1	RUVB1_MOUSE	1.41	1.12	1.52	1.38	1.09	1.31
Adenine phosphoribosyltransferase	APT_MUSPA	0.48	0.93	0.54	0.57	0.89	0.58
Glutathione reductase, mitochondrial	GSHR_MOUSE	1.43	0.91	1.52	1.06	0.83	1.01
Phosphoenolpyruvate carboxykinase (GTP), mitochondrial	POKGM_MOUSE	1.87	0.85	1.81	1.75	0.88	1.60
Response gene to complement 32 protein	RGC32_MOUSE	0.46	1.37	0.70	---	---	---
Thymosin beta-10.	TYB10_MOUSE	3.45	1.08	4.01	7.07	0.92	9.06
Mitotic spindle assembly checkpoint protein MAD2A	MD2L1_MOUSE	1.50	1.20	1.55	---	---	---
Glycyl-tRNA synthetase	SYG_MOUSE	1.43	1.00	1.33	1.50	1.01	1.54
Chromobox protein homolog 3	OBX3_MOUSE	1.46	0.98	1.39	1.60	1.07	1.66
cAMP effect
BTB/POZ domain-containing protein TNFAIP1	TNAP1_MOUSE	1.14	1.70	1.74	---	---	---
UPF0565 protein	U566_MOUSE	1.06	1.71	1.79	---	---	---
T-complex protein 1 subunit delta	TCPD_MOUSE	1.09	1.50	1.73	1.03	1.16	1.21
combined (cAMP and mutational) effect
Histone H1.1	H11_MOUSE	1.29	1.37	1.54	---	---	---
Histone H1.2	H12_MOUSE	1.39	1.43	1.65	1.26	1.30	1.63
Histone H1.3	H13_MOUSE	1.38	1.45	1.66	1.30	1.37	1.71
Thioredoxin	THIO_MOUSE	1.03	0.97	1.39	1.32	1.17	1.62
Proteasome subunit alpha type-6	PSA6_MOUSE	1.14	1.24	1.54	1.21	1.39	1.63
Proteasome subunit alpha type-4	PSA4_MOUSE	1.12	1.38	2.12	---	---	---
Ab1 interactor 1	ABI1_MOUSE	0.72	0.73	0.46	---	---	---
Neurabin-2	NEB2_MOUSE	0.78	0.96	0.48	---	---	---
Actin-related protein 2	ARP2_MOUSE	1.31	1.27	1.47	1.42	1.33	1.63

Note: - - - indicates not detected.