Table 3.

Summary of the urine and blood-associated clinical proteomic studies highlighted in this review

Liquid biopsy	Protein quantitation	MS model	Sample preparation	Clinical question	Proteins detected	Patient cohort	References
Plasma	Isotopic label	LTQ Orbitrap	Immunodepletion, filtration, SCX fractionation	Pancreatic cancer, pancreatitis and healthy control plasma	1300	3	[156]
	Label-free DDA	LTQ Orbitrap & 5500 Q-trap	PDX, N-glycopeptide enrichment, SRM validation in human sera	Ovarian cancer biomarker development	906	224	[175]
	Label-free SWATH	5600 TOF	Immunodepletion, SCX, SAX, RPF, size-exclusion chromatography	Early diagnosis of CRC	427	100	[159]
		5600 TOF	N-glycopeptide enrichment, Off-gel fractionation	Five different cancer types and their matched controls	1151	284	[172]
Serum	Label-free DDA	LTQ Orbitrap	PDX, N-glycopeptide enrichment, Targeted validation in human	PCa diagnosis	775	8	[173]
		QE HF	PDX, N-glycopeptide enrichment, PRM validation in human sera	High grade serious ovarian cancer biomarkers and longitudinal monitoring	2200	20	[87]
	iTRAQ	5600 TOF	Immunodepletion, SWATH verification	Proteins leaving lung cancer tumours into pulmonary veins	1000	50	[158]
Urine	Label-free DDA	5600 TOF	Gel fractionation, RPF, IEF	Characterization of the healthy urine proteome	6085	24	[176]
		QE	MW-filtration, SCX, PRM validation	Renal cell carcinoma prognostic biomarkers	2589	115	[183]
		LTQ	Gel fractionation	Identify novel therapeutic targets for Wilms tumour	6520	49	[184]
		QE	Gel fractionation	Profiling urine from lung cancer patients and other tumors	7408	46	[185]
Post-DRE urine	iTRAQ	OV	Ultracentrifugation, RPF	Discovery of new biomarker for high Gleason PCa	4710	18	[191]
	Label-free DDA	QE	Ultracentrifugation	Characterizing EVs from EPS in urine from PCa and healthy patients	877	24	[189]
	SRM	TSQ Vantage	MW filtration, TFE	Targeted proteomics identifies signatures for extracapsular prostate cancer	232	74	[188]
		Qtrap5500	FASP	Biomarker validation for early detection and stratification of PCa	64	107	[192]