Table II. Identified CNS lupus-specific proteins by immunoprecipitation followed by LC-MS/MS shotgun analysis of whole human brain and human brain tumor cell line total protein. CNS, central nervous system; LC-MS/MS, liquid chromatography-tandem mass spectrometry.

Testa	Protein nameb	Accession No.
1	3-hydroxyacyl-CoA dehydrogenase type-2	NP_004484.1
1	40S ribosomal protein S24 isoform c	NP_001017.1
1	40S ribosomal protein S5	NP_001000.2
1	Actin, α skeletal muscle	NP_001091.1
1	ATP synthase subunit β, mitochondrial precursor	NP_001677.2
1	ATPase family AAA domain-containing protein 3A isoform 1	NP_060658.3
1	ATP-dependent RNA helicase DDX1	NP_004930.1
1	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3	NP_001347.3
1	DNA-(apurinic or apyrimidinic site) lyase	NP_001632.2
1	Nuclear factor 1 A-type isoform 2	NP_005586.1
1	Polyadenylate-binding protein 4 isoform 2	NP_003810.1
1	Replication protein A 14 kDa subunit	NP_002938.1
1	RNA-binding protein 14	NP_006319.1
1	Tubulin alpha-1A chain	NP_006000.2
2	14–3-3 protein ζ/Δ	NP_003397.1
2	39S ribosomal protein L12, mitochondrial precursor	NP_002940.2
2	40S ribosomal protein S12	NP_001007.2
2	Actin, cytoplasmic 1	NP_001092.1
2	α-enolase	NP_001419.1
2	ATP-dependent RNA helicase A	NP_001348.2
2	Creatine kinase B-type	NP_001814.2
2	Elongation factor 1-α1	NP_001393.1
2	Glial fibrillary acidic protein isoform 1	NP_002046.1
2	Glucose-6-phosphate isomerase isoform 2	NP_000166.2
2	Glyceraldehyde-3-phosphate dehydrogenase	NP_002037.2
2	Heat shock cognate 71 kDa protein isoform 1	NP_006588.1
2	Heat shock protein HSP 90-β	NP_031381.2
2	Histone H2A type 1	NP_003500.1
2	Histone H4	NP_003529.1
2	Hypothetical protein LOC348262	NP_997251.2
2	Keratin, type I cytoskeletal 10	NP_000412.3
2	Keratin, type II cytoskeletal 1	NP_006112.3
2	l-lactate dehydrogenase A chain isoform 1	NP_005557.1
2	NEFA-interacting nuclear protein NIP30	NP_079222.1
2	Nuclear factor 1 C-type isoform 1	NP_005588.2
2	Peptidyl-prolyl cis-trans isomerase A	NP_066953.1
2	Phosphoglycerate mutase 1	NP_002620.1
2	Probable ATP-dependent RNA helicase DDX5	NP_004387.1
2	Probable ATP-dependent RNA helicase DDX6	NP_004388.2
2	Programmed cell death protein 6	NP_037364.1
2	Pyruvate kinase isozymes M1/M2 isoform M2	NP_002645.3
2	Small nuclear ribonucleoprotein-associated proteins B and B' isoform B	NP_003082.1
2	SWI/SNF complex subunit SMARCC1	NP_003065.3
2	T-complex protein 1 subunit eta isoform a	NP_006420.1
2	THO complex subunit 4	NP_005773.3
2	U1 small nuclear ribonucleoprotein 70 kDa	NP_003080.2
1, 2	60 kDa heat shock protein, mitochondrial	NP_002147.2
1, 2	Proteasome activator complex subunit 3 isoform 1	NP_005780.2
1, 2	Ribonuclease P protein subunit p30 isoform b	NP_006404.1
1, 2	Tubulin β chain	NP_821133.1

^a These numbers show in which 2 LC-MS/MS shotgun analyses the proteins were identified.

^b Protein identification was based on the criterion of having at least one MS/MS data with Mascot scores that exceeded the thresholds (p < 0.05).