Table1.

Proteomics-based biomarker discovery in different biological fluids such as blood (plasma or serum), CSF, urine, saliva, CSF and tissue/ or cells

Sample/ Disease	Method	Potential biomarker	Study
Serum DS Epilepsia	2D-DIGE, 2D-CF, MudPIT; LC/LC-MS/MS, MALDI-TOF-MS MS, ELISA	Alpha-1-acid, glycoprotein SAA	Nagalla et al., 2007 (63) Li et al., 2013 (64)
Plasma PD Neuroblastoma AD Gastric cancer	iTRAQ, MALDI-TOF-TOF, MRM, LC-MS/MS LC-MS/MS iTRAQ-MS, ELISA 2DE-MS, WB	Tyrosine-kinase, non-receptor-type 13, Netrin G1 Complement C3 Complement 4a CFI precursor	Lehnert et al., 2012 (65) Kim et al. 2014 (66) Bennett et al., 2012 (67) Liu et al., 2007 (68)
Urine ADPKD Bladder cancer FSGS	CE-MS Shotgun proteomics, ELISA nLC-MS/MS	PKD1, PKD2 Midkine, HA-1 77 putative biomarker such as: CD59, CD44, IBP7, Robo4, and DPEP1	Kistler et al., 2009, 2013 (69, 70) Shimwell al., 2014 (71)
Saliva Diabetes type2 OSCC Gastric cancer Oral Cancer GCF Periodontal disease	2D-LC-MS/MS, WB SDS-PAGE, LC-MS/MS tandem mass tags (TMT) shotgun proteomics LC-MS/MS	G3P, SAA, PLUNC, TREE resistin (RETN) CSTB, TPI1, DMBT1 M2BP, MRP14, CD59, Profilin, Catalase Moesin	Border et al., 2012 (72) Wu et al., 2015 (73) Xiao et al., 2016 (74) Hu et al., 2008 (75) Tsuchida et al., 2014 (76)
CSF AD Multiple sclerosis	Nano-LC-MRM/MS, ELISA 2DE-MS	24 peptides CRTAC-1B,tetranectin	Choi et al., 2013 (77) Hammack et al.,2004 (78)
Tissue Breast cancer Colon Cancer BCC cell culture media REH cell line	iTRAQ, SRM/MRM, LC-MS/MS, WB, IHC Label-free LC-MS/MS, WB, IHC 2DE-MS- MALDI 2DE-MALDI-TOF/TOF-MS	GP2, MFAP4 RAI3 C3b,aldolase C, FGG, Prx-cis, Protrombin, VDAC and LRG VDAC1, SNX3, PFDN6	Muraoka et al., 2012 (79) Zougman et al., 2013 (80) Zali et al., 2010 (81) Dehghan-Nayeri et al., 2016 (82)

AD (Alzheimer disease), PD (parkinson disease), ADPKD (autosomal dominant polycystic kidney disease), OSCC (oral squamous cell carcinoma), CSTB (cystatin B), TPI1 (triosephosphate isomerase), DMBT1 (deleted in malignant brain tumors 1 protein). FSGS (Focal Segmental Glomerulosclerosis), BCC (Basal Cell Carcinoma), VDAC1 (voltage dependent anion channel 1), SNX3 (sorting Nexin 3), PFDN6 (prefoldin subunit 6), GCF (Gingival Crevicular Fluid).