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Table 2 Summary of the clinical proteogenomic studies highlighted in this review

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

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]