Table 2.
Reported applications of DIA to solid tissues in cancer proteomics
| Reference | Solid tissues evaluateda | Protein analysis results | Highlight(s) |
|---|---|---|---|
| Hou 2015 (155) | Paired tissues: Esophageal squamous cell carcinoma tissue and adjacent normal tissue (n = 10, frozen tissues only) | 1758 proteins quantified; 467 proteins differentially expressed | High correlation between quantitative information derived from DIA (SWATH) and co-performed MRM experiments |
| Gao 2017 (160) | Paired tissues: Hepatocellular carcinoma (HBV-associated) and adjacent normal liver tissue (discovery set n = 14, verification set n = 6, frozen tissues only) | 4216 unique proteins quantified; 338 differentially expressed | Aspects of metabolic reprogramming identified; DIA (SWATH) data consistent with previous western-blot/IHC-validated results |
| Schwarzfischer 2017 (156) | Burkitt lymphoma: 5 frozen, 5 FFPE DLBCL: 6 frozen, 9 FFPE |
Frozen: 2938 proteins quantified, 1125 differentially regulated FFPE: 1442 proteins quantified, 404 differentially regulated |
Quantitative results reproducible between frozen and FFPE tissues; corroborating metabolomic studies were performed, demonstrating high secretion of pyruvic acid in BL compared to DLBCL |
| Keam 2018 (158) | Paired tissues: Prostate cancer (PCa), before and 14 days after radiation therapy (n = 8 patietns, comprising 2 with frozen and FFPE tissue, 1 frozen only, 5 FFPE only) | >5000 proteins quantified, 49 differentially expressed | Deeper proteomic analyses obtained for prostatic tissue by DIA compared to previously reported MS pipeline applied to PCa (159) |
| Zhu 2019 (4) | Multiple prostate cancer cohorts (frozen and FFPE tissues); multiple diffuse large B-cell lymphoma cohorts (n = 41 patients in first cohort, n = 52 patients in second cohort, 113 FFPE samples) | 3030 proteins quantified in one PCa cohort, 4144 proteins in second cohort | Panel of protein biomarker candidates identified for PCa diagnosis; myeloperoxidase identified as prognostic marker in DLBCL |
| Janacova 2020 (161) | Endometrial cancer (n = 34, all FFPE): 15 – previous tamoxifen treatment (ET) 19 – no previous tamoxifen (EN) 11 – adjacent myometrium |
904 proteins quantified; Differential expression of calcyphosin (CAPS) and stathmin confirmed (STMN1) | CAPS and STMN1 also appeared useful as prognostic indicators |
| Marchione 2020 (159) | 18 tissue types evaluated using HYPERsol protocol + separate analyses of 32 archival samples of malignant peripheral nerve sheath tumor (MPNST), melanoma, and synovial sarcoma | 4000–5000 proteins/sample | DIA-based analyses applied to distinguish histomorphologic mimics |
| Weke 2022 (157) | Glioblastoma (GBM) FFPE microdissections (n = 5) | >1700 proteins identified; >1400 quantified | Leveraged multiple sample processing approaches; Protein identifications increased compared to DDA; High quantitative precision for GBM markers: GFAP, FN1, VIM, and MBP |
Abbreviations: BL, Burkitt’s lymphoma; DLBCL, diffuse large B-cell lymphoma; HYPERSol, high-yield protein extraction and recovery by direct solubilization; MPNST, malignant peripheral nerve sheath tumor; MRM, multiple reaction monitoring; PCa, prostate cancer; SWATH, sequential window acquisition of all theoretical spectral.
High-yield protein extraction and recovery by direct solubilization.
a
Samples other than solid tissues are excluded from this table.