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] |