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Table 1 Summary of select tissue-centric proteomic studies highlighted in this review

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

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]