. Author manuscript; available in PMC: 2015 Jan 22.

Published in final edited form as: Proteomics. 2008 Aug;8(15):3061–3070. doi: 10.1002/pmic.200700715

Table 1.

LPS-induced differentially regulated proteins in the macrophage pair.

Accession Number	Protein Description	Molecular Function / Biological Process^a	Subcellular Location ^b	Number of Peptides for Quantification	GG2EE (TLR4 deficient) +LPS		HeNC2 (TLR4 functional) +LPS
					lysine-d₄ unlabeled	S.D. ^c	lysine- ¹³C₆¹⁵N₂ : unlabeled	S.D. ^c

gi\|31981657	carbonic anhydrase 2	reversible hydration of carbon dioxide; zinc ion binding	cytoplasmic	5	3.18	0.65	54.73	8.01
gi\|6680415	interleukin 1 beta	cytokine activity; cell proliferation; Inflammatory response	extracellular	2	1.01	0.11	24.58	2.66
gi\|31981909	aldo-keto reductase family 1, member B3	aldehyde reductase activity; Oxidoreductase activity	cytoplasmic	2	1.01	0.10	7.84	0.63
gi\|6754450	fatty acid binding protein 5	glucose/lipid metabolism; phosphatidylcholine biosynthesis	cytoplasmic mitochondrial	2	1.18	0.03	2.05	0.12
gi\|21644585	2'-5' oligoadenylate synthetase 3	nucleic acid binding	cytoplasmic nuclear	1	1.45	/	2.00	/
gi\|6671666	CAP, adenylate cyclase-associated protein 1	cellular morphogenesis; receptor mediated endocytosis; Actin cytoskeleton organization and biogenesis	membrane	4	1.19	0.09	1.68	0.16
gi\|6680457	Inositol polyphosphate-1- phosphatase	Phosphatidylinositol signaling; magnesium ion binding	cytoplasmic nuclear	2	1.08	0.02	1.86	0.12
gi\|6679601	RAS-related C3 botulinum substrate 2	small GTPase mediated signal transduction	cytoplasmic; membrane- associated when activated	2	0.92	0.17	1.73	0.15
gi\|31543778	signal transducer and activator of transcription 1	intracellular signaling cascade; Regulation of transcription, DNA- dependent	cytoplasmic; translocated into the nucleus in response to phosphorylatio n	2	1.68	0.08	2.54	0.06
gi\|7305169	heat shock protein 105	chaperone cofactor dependent protein folding; ATP binding	cytoplasmic	2	1.07	0.11	1.70	0.08
gi\|9910568	BCR downstream signaling 1	protein tyrosine kinase signaling pathway; intracellular signaling cascade; myeloid cell differentiation	mitochondrial cytoplasmic	1	1.54	/	1.76	/
gi\|38090997	methionine-tRNA synthetase	protein biosynthesis; TRNA aminoacylation for protein translation	mitochondrial	2	1.71	0.17	1.48	0.11
gi\|47894398	tropomyosin 4	actin binding; muscle development	mitochondrial nucelar	3	0.92	0.09	1.63	0.11
gi\|12963663	magnesium-dependent phosphatase-1	/	cytoplasmic	1	0.73	/	1.36	/
gi\|40254244	loss of heterozygosity 11	DNA repair; pathogenesis; cell cycle	nuclear	1	0.82	/	1.75	/
gi\|13624317	interleukin 1 receptor antagonist	immune response; cell surface receptor linked signal transduction; lipid metabolism	extracellular integral to plasma membrane	1	0.49	/	1.48	/
gi\|34328230	adenylate kinase 2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	Mitochondrial Intermembrane space		0.89	0.05	1.48	0.06
gi\|7949047	hydroxyacyl- Coenzyme A dehydrogenase type II	oxidoreductase activity	mitochondrial cytoplasmic	1	0.95	/	1.34	/
gi\|6678483	ubiquitin-activating enzyme E1	ubiquitin-dependent protein catabolism	cytoplasmic vesicles of secretory system	1	1.02	/	1.33	/
gi\|6680187	hematopoietic cell specific Lyn substrate	substrate of the antigen receptor-coupled tyrosine kinase	mitochondrial	2	0.71	0.05	1.39	0.01
gi\|6671509	actin beta		cytoplasmic	4	0.99	0.05	1.00	0.09
gi\|6671549	peroxiredoxin 6	redox regulation of the cell; response to reactive oxygen species	cytoplasmic	7	1.02	0.05	0.73	0.06
gi\|30519911	transgelin 2	muscle development	nuclear	3	0.97	0.17	0.54	0.08
gi\|6755114	peroxiredoxin 5	antioxidant protein with alkyl hydroperoxidase activity	cytoplasmic	7	0.52	0.03	0.51	0.11
gi\|7106301	microtubule- associated protein	mitosis; cell cycle	microtubule Golgi apparatus	2	1.04	0.10	0.50	0.02
gi\|24762230	ribosomal protein S15a	protein translation	cytoplasmic	2	0.93	0.07	0.49	0.10
gi\|6755682	serine/threonine kinase receptor associated protein (Strap)	negative regulation of transcription from RNA polymerase II promoter; negative regulation of transforming growth factor beta receptor signaling pathway	cytoplasmic mitochondrial	3	1.00	0.04	0.48	0.04
gi\|6680047	guanine nucleotide binding protein beta 2	protein kinase C binding; protein localization; intracellular signaling cascade	cytoplasmic	2	1.00	0.08	0.46	0.06
gi\|42476345	ribosomal protein large P2	tanslational elongation	extracellular	3	1.04	0.07	0.44	0.05
gi\|31981458	glutaredoxin 1	cell redox homeostasis; electron transport	cytoplasmic		0.89	0.05	0.40	0.06
gi\|51829008	protein phosphatase 2A inhibitor-2	DNA replication; Cellular physiological process	nuclear	2	1.05	0.06	0.36	0.01
gi\|6754570	annexin A1	calcium ion binding; regulation of cell proliferation	cytoplasmic	4	0.31	0.15	0.33	0.08
gi\|9789995	stathmin 1	mitotic spindle organization and biogenesis; microtubule depolymerization; intracellular signaling cascade	cytoplasmic	3	0.95	0.03	0.22	0.04
gi\|6753060	annexin A5	calcium ion binding; calcium-dependent phospholipid binding	cytoplasmic	2	0.31	0.14	0.21	0.08
gi\|25023967	endothelial monocyte- activating polypeptide	calcium ion binding; cytokine activity	nuclear	2	0.50	0.01	0.21	0.05

Functional annotation was extracted from Swissprot database;

Subcellular location was obtained from swissprot database if such information is available. PSORT II (http://psort.nibb.ac.jp) was used to predict the subcellular location if no information exists in Swissprot.

Standard Deviation was calculated from the quantification ratio of several peptides. “/” indicates the quantification ratio is obtained from one lysine containing peptide.