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

Label-free DDA

FFPE

GEN, TRA, PHO

OF

FASP, RPF

Stratify HBV-related hepatocarcinoma into subtypes

[137]

FF

EPI, TRA, PHO

OF

Urea, RPF, Super-SILAC

Distinguishing between four subgroups of medulloblastomas

[140]

GEN, EPI, TRA

QE

TFE

Biomarkers of curable PCa

[6]

OCT

TRA, EPI

OV

TFE

CRC characterization

[4]

GEN, TRA, PHO

QE

Urea, RPF, TMT additional

Tumour, adjacent healthy tissue and blood in colon cancer patients

[79]

Label-free SWATH

OCT

TRA

5600 TOF

Pressure cycling technology, urea

Protein degradation rates in PCa and adjacent healthy tissue

[91]

FF

GEN, EPI, TRA

5600 TOF

RIPA buffer

Untreated and castration-resistant PCa compared to benign

[138]

Isobaric Labelling

FFPE

GEN, TRA

QE

FASP and IEF, TMT

Recapitulating breast cancer subtypes

[135]

FF

GEN, TRA, PHO

QE HF

SDS, FASP, RPF, TMT

Tissue and blood samples from HBV-related hepatocarcinoma and healthy adjacent liver patients

[139]

GEN, TRA

QE

FASP and IEF, TMT

Characterizing pathogenetic impact of hyperdiploidy in acute lymphoblastic leukemia

[142]

GEN, TRA, PHOS, GLYCO

QE

SDS, RPF, iTRAQ

Characterization of gastric cancer from tumour, healthy adjacent tissue and blood samples

[141]

OCT

GEN, TRA, PHO

OF Lumos

Urea, Basic RPF, TMT

Characterization of treatment-naïve clear cell renal cell carcinoma

[139]

GEN, TRA, PHO

LTQ Velos

TFE. iTRAQ

High-grade serous ovarian carcinoma characterization

[5]

GEN, TRA, PHO

QE

Urea, basic RPF, iTRAQ

Characterization of breast cancer subtypes: basal, HER2-enriched, luminal A, luminal B

[3]