Table 2.

Summary of the clinical proteogenomic studies highlighted in this review

Protein quantitation	Tissue type	Additional omic datasets	MS model	Sample preparation	Clinical question	Proteins detected	Patient cohort	References
Label-free DDA	FFPE	GEN, TRA, PHO	OF	FASP, RPF	Stratify HBV-related hepatocarcinoma into subtypes	9252	110	[137]
	FF	EPI, TRA, PHO	OF	Urea, RPF, Super-SILAC	Distinguishing between four subgroups of medulloblastomas	3892	41	[140]
		GEN, EPI, TRA	QE	TFE	Biomarkers of curable PCa	7054	76	[6]
	OCT	TRA, EPI	OV	TFE	CRC characterization	7526	95	[4]
		GEN, TRA, PHO	QE	Urea, RPF, TMT additional	Tumour, adjacent healthy tissue and blood in colon cancer patients	8067	110	[79]
Label-free SWATH	OCT	TRA	5600 TOF	Pressure cycling technology, urea	Protein degradation rates in PCa and adjacent healthy tissue	3056	68	[91]
	FF	GEN, EPI, TRA	5600 TOF	RIPA buffer	Untreated and castration-resistant PCa compared to benign	4601	38	[138]
Isobaric Labelling	FFPE	GEN, TRA	QE	FASP and IEF, TMT	Recapitulating breast cancer subtypes	9995	45	[135]
	FF	GEN, TRA, PHO	QE HF	SDS, FASP, RPF, TMT	Tissue and blood samples from HBV-related hepatocarcinoma and healthy adjacent liver patients	10,783	159	[139]
		GEN, TRA	QE	FASP and IEF, TMT	Characterizing pathogenetic impact of hyperdiploidy in acute lymphoblastic leukemia	8480	89	[142]
		GEN, TRA, PHOS, GLYCO	QE	SDS, RPF, iTRAQ	Characterization of gastric cancer from tumour, healthy adjacent tissue and blood samples	9625	80	[141]
	OCT	GEN, TRA, PHO	OF Lumos	Urea, Basic RPF, TMT	Characterization of treatment-naïve clear cell renal cell carcinoma	11,355	103	[139]
		GEN, TRA, PHO	LTQ Velos	TFE. iTRAQ	High-grade serous ovarian carcinoma characterization	9600	174	[5]
		GEN, TRA, PHO	QE	Urea, basic RPF, iTRAQ	Characterization of breast cancer subtypes: basal, HER2-enriched, luminal A, luminal B	12,405	77	[3]