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Table 3 Summary of the urine and blood-associated clinical proteomic studies highlighted in this review

From: Recent advances in mass spectrometry based clinical proteomics: applications to cancer research

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]