Table 1.

Summary of select tissue-centric proteomic studies highlighted in this review

Protein quantitation	Tissue type	Sample preparation	MS Model	Clinical question	Proteins detected	Patient cohort	References
Label-free DDA	FFPE	FASP, SAX	QE	CRC, healthy tissue and adenoma	10,000	32	[26]
			QE	Malignant vs. benign prostate tissue	9000	36	[31]
			QE	Breast cancer heterogeneity and triple-negative subtypes	10,819	131	[92]
		FASP, SAX, Super-SILAC normalization	QE	ER-positive luminal breast cancer progression and metastasis	10,000	88	[77]
			QE	Breast cancer subtypes	10,000	40	[93]
			QE HF	Melanoma response to immunotherapy	10,300	116	[95]
		SDS	QE	Ovarian cancer chemosensivity and chemoresistance mediators	9000	25	[105]
		Phospho-enrichment	QE	Triple-negative breast cancer treatment outcomes	2643	34	[110]
		TFE	QE HF	Metabolic regulators of CAF’s in high-grade serous carcinoma	6944	107	[24]
		FASP, SAX, LCM	LTQ XL	Colon cancer with healthy matched	6000	6	[29]
		MudPIT	LTQ XL	HPV-positive and HPV negative oropharyngeal carcinomas	2633	53	[101]
	FF	FASP, SAX	QE	PCa bone metastasis characterization	5067	22	[32]
		Urea, SDS, CHCl3/MeOH precipitation	QE	Ovarian carcinoma histotypes	6360	20	[100]
		iST	QE HF	Primary urachal carcinoma, metastases and healthy tissue	5543	1	[96]
Label-free SWATH	OCT	Pressure-cycling technology, urea	5600 TOF	Intratumoural heterogeneity of PCa	6873	60	[90]
	FF		5600 TOF	Renal cell carcinoma and healthy controls	4624	18	[103]
			5600 TOF	Hepatocellular carcinoma and healthy adjacent control	2579	38	[104]
		FASP	5600 TOF	Breast cancer classification	2842	96	[102]
Isobaric Labelling	FFPE	SP3, RPF, TMT	OF	High grade serous and clear cell ovarian carcinomas	8167	20	[42]
	FF	PDX, iTRAQ	OV, QE	Basal and luminal-B breast cancer subtypes	8126	2	[134]
		FASP, RPF, iTRAQ	OV	Non-muscle invasive and muscle invasive bladder cancer	900	8	[84]
		RPF, glyco-enrichment, iTRAQ	OV	Ovarian high-grade serous carcinoma and benign cases	4817	6	[99]
		Urea, glyco- enrichment, iTRAQ	QE	Squamous cell carcinoma vs. adenocarcinoma and healthy controls	8337	18	[106]
		PDX, phospho-enrichment, TMT	OF Lumos	Luminal and basal breast cancer subtypes	7700	4	[109]