Table 2.

Summary of identified biomarkers in different specimen types

Specimen type	Disease association	Biomarkers	Reference
Serum	SLE	m/z ratio 4070.09, 7770.45, 28045.1, 3376.02; Apolipoprotein A‐I, prothrombin, keratin type II (cytoskeletal), keratin 1, albumin, type II keratin, transthyretin, haptoglobin 2; m/z ratio 9342.23, 4094.03, 5905.35, 7973.53	Huang et al. 12 Kazemipour et al. 14 Wu et al. 40
	LN	Annexin A2 antibody, ATP synthase subunit‐alpha, mitochondrial, ATP synthase subunit‐beta, mitochondrial, alpha‐enolase ENO1, Moesin, glyceraldehyde‐3‐phosphate dehydrogenase, Elongation factor 1‐alpha 1, guanine nucleotide‐binding protein G(i) subunit‐alpha‐2, isoform 2 of AP‐2 complex subunit mu, isoform 2 of protein disulphide isomerase A6, pyruvate kinase PKM, 60‐kD heat‐shock protein mitochondrial, actin‐related protein 3, V‐type proton ATPase subunit B brain isoform, myosin‐9, isoform 3 of heterogeneous nuclear ribonucleoprotein, septin‐7, isoform 2 of coronin‐1C, tubulin‐beta‐4A chain, T‐complex protein 1 subunit‐gamma, isoform 2 of ATP‐dependent RNA helicase, isoform 2 of basigin, dolichyl‐diphosphooligosaccharide–protein glycosyltransferase 48‐kD subunit, heat‐shock protein HSP 90‐beta, ezrin, isoform 2 of neutral cholesterol ester hydrolase 1, isoform 2 of heat‐shock cognate 71‐kD protein, heterogeneous nuclear ribonucleoprotein U, Rho GTPase‐activating protein 1, isoform 2 of fatty aldehyde dehydrogenase, serine palmitoyltransferase 1, isoform 2 of ATP‐citrate synthase; IgM heavy chain, apolipoprotein CIII, HSA fragment, haemopexin fragment; glyceraldehyde‐3‐phosphate dehydrogenase, heterogeneous nuclear ribonucleoprotein A2/B1, annexin A2, aldolase A, elongation factor 1‐gamma, lupus La protein (SS‐B/La); m/z 4207 Da, 2658 Da, 1465 Da, 5332 Da, 5900 Da, 1943 Da	Caster et al. 11 Morgan et al. 16 Serada et al. 17 Zhou et al. 18
	CNS‐SLE	Peroxiredoxin‐4, ubiquitin carboxyl‐terminal hydrolase isozyme L1, splicing factor arginine/serine‐rich 3, histone H2A type 1	Iizuka et al. 13
	NPSLE	Stress‐70 protein, Rab guanosine diphosphate dissociation inhibitor α antibody, Isocitrate dehydrogenase [NAD] subunit‐alpha, L‐lactate dehydrogenase B chain, F‐actin‐capping protein subunit‐alpha‐2, Rab guanosine diphosphate dissociation inhibitor‐beta	Kimura et al. 15
PBMCs	SLE	Immunoglobulin J chain, apolipoprotein A‐IV precursor, glutathione S‐transferase, calprotectin L1H, zinc finger protein subfamily 1A; high‐mobility group box protein 1 (CD4+ T cells); S100 calcium‐binding protein A9, heat‐shock protein 90α/β, heat‐shock protein 70, peptidyl‐prolyl cis‐trans isomerase A; serine‐threonine kinase receptor‐associated protein; cDNA FLJ61039, AF4/FMR2 family member 1, cDNA FLJ55107, structural maintenance of chromosome protein 3, protein S100‐A9, protein S100‐A8, protein S100‐A12, lysozyme C, glutathione S‐transferase kappa 1 isoform c, isoform 2 of zinc finger protein 549, 26‐kD protein, histone H2A type 1, myeloblastin, brain acid‐soluble protein 1, protein S100‐P, neutrophil defensin 1, isoform 2 of metalloendopeptidase OMA1 (mitochondrial), 42‐kD protein, latent transforming growth factor‐beta‐binding protein 1 isoform, resistin, AF4/FMR2 family member 1, cDNA FLJ61340, HLA class I histocompatibility‐alpha chain, histone H1.2, cDNA FLJ51589, putative uncharacterized protein GCA, FCGR3B protein, nucleolar protein 5A, serine‐threonine kinase receptor‐associated protein, myosin regulatory light polypeptide 9, isoform A of bromodomain and WD repeat‐containing protein 1, vacuolar protein sorting‐associated protein 35, putative uncharacterized protein PTMA, isoform 2 of retinol dehydrogenase 11, ribosomal protein L10 (fragment), cathepsin A isoform a precursor, high‐mobility group protein B2, protein disulphide isomerase A4, 17‐kD protein, NADH dehydrogenase [ubiquinone] 1‐alpha subcomplex subunit 4, isoform 1 of multimerin‐1, p180/ribosome receptor, NUMA1 variant protein (fragment), 20‐kD protein, dihydrolipoyllysine residue succinyltransferase component of 2‐oxogluterate dehydrogenase complex (mitochondrial), isoform 2 of heterochromatin protein 1‐binding protein 3, 16‐kD protein, cDNA FLJ51702, myosin regulatory light chain MRCL2 isoform B, apolipoprotein C‐I, MHC class I antigen (fragment), protein XRP2, tubulin‐alpha‐1B chain, Ras‐related C3 botulinum toxin substrate 2, leucocyte antigen HLA‐A, 51‐kD protein, HLA class I histocompatibility antigen (B‐58‐alpha chain), isoform 2 of retinol dehydrogenase 11, ribosomal protein L10 (fragment), cDNA FLJ55509, platelet basic protein, membrane‐associated progesterone receptor component 1, hypothetical protein XP_02342881, isoform 1 of reticulon‐4, putative uncharacterized protein PARVB, isoform 1 of protein unc‐13 homologue D, putative uncharacterized protein LCN2, cathelicidin antimicrobial peptide precursor, 66‐kD protein	Dai et al. 19 Li et al. 20 Pavon et al. 21 Wang et al. 22 Wang et al. 23
	SLE Thrombophilia	Annexin A5, glyceraldehyde‐3‐phosphate dehydrogenase, integrin‐linked protein kinase, adenylylcyclase‐associated protein 1, transketolase, proline‐serine‐threonine phosphatase‐interacting protein 2, triosephosphate isomerase, tyrosine‐protein kinase CSK, dynamin‐1‐like protein, elongation factor 1‐alpha 1, T‐complex protein 1 subunit zeta, heat‐shock protein‐beta‐1, phosphoglycerate kinase 1, alpha‐enolase, osteoclast‐stimulating factor 1, heat‐shock cognate 71 kD protein	Zhou et al. 24
Platelet‐poor plasma	SLE	IgG‐MPs, IgM‐MPs, C1q‐MPs (proteins discussed by the author out of 248 proteins)	Nielsen et al. 25 Ostergaard et al. 27
Urine	LN	MP‐G3BP, MP‐C1q (3 subunits), MP‐Ig (most abundant: IgJ, IgM, IgG2), Ig (IgG, IgM, IgA), complement proteins (C1), fibronectin, 14‐3‐3η, desmosomal proteins, ficolin 2, galectin‐3‐binding protein, β2‐glycoprotein I, β6‐tubulin, β2C‐tubulin, lysosome‐associated membrane protein 1, transforming factor β1; m/z ratio 3340, 3980; prostaglandin H 2 D‐isomerase, serotransferrin, alpha‐1‐glucoprotein, alpha‐2‐HS‐glycoprotein, haptoglobin, alpha‐1‐antitrypsin, albumin, Zn‐alpha‐2‐glycoprotein, Ig kappa chain V‐III SLE region, Ig kappa chain V‐III HAH region, Ig kappa chain C region, retinol‐binding protein 4, beta‐2‐microglobulin, transthyretin, hepcidin (isoforms 20 and 25), a1‐antitrypsin, N‐terminal region of albumin	Nielsen et al. 25 Mosley et al. 29 Somparn et al. 30 Zhang et al. 31
Biopsies	LN	Renal: Ezrin P81, serotransferrin, cytokeratin 18, cytokeratin 19, alpha‐1‐antitrypsin, albumin, plasma glutathione peroxidase, 1433 protein epsilon, annexin A5; heterogeneous nuclear ribonucleoproteins A2/B1 isoform B1, lamin A protein, mimecan preproprotein, annexin A1, annexin A2 isoform 2, alpha‐1‐antitrypsin precursor, glutathione S‐transferase‐P1c, adenine phosphoribosyltransferase isoform a, collagen type VI alpha‐3 (isoform CRA_h), formiminotransferase cyclodeaminase form C, aldolase B, aldehyde dehydrogenase, 2‐oxoglutarate dehydrogenase (mitochondrial isoform 1 precursor), L‐arginine:glycine amidinotransferase, pyrroline‐5‐carboxylate dehydrogenase, antiquitin	Alaiya et al. 32 Sui et al. 33
	SLE Skin lesions	Skin: keratin 10, keratin 16, keratin 14, Keratin 6, keratin 5, keratin 2e, keratin 1, involucrin	Fang et al. 35
CSF	CNS‐SLE	m/z peaks 8595 (ubiquitin), 7170, 7661, 7740, 5806	Sun et al. 36

Only highlighted (bold) proteins in table were validated by the authors.