Table 1 Key application features of proteomics technologies for cancer liquid biopsies
| Â | Basic principles | Typical multi-plexity | Typical sample throughput (per assay) | Limit of Detection/ Dynamic range | Readout | De-novo/ targeted | Laboratory procedures | Advantages | Limitations |
|---|---|---|---|---|---|---|---|---|---|
Mass Spec (MS) | Samples are prepared according to specific purposes, followed by digestion, peptide ionization, and tandem MS scans. | ~ 6500 (Urine) ~ 1500 (blood) | Up to 16 (TMT labelling) | Picogram/ 4-5 logs | Fragmented peptide sequences and spectrum counting | De-novo/ Targeted | Heavy instrumentation and non-standardized workflows for pre-MS sample preparation Semi-automated | De-novo process suitable for exploratory research | Low throughput, Complex depletion process, limitations to analyze protein PTMs |
Antibody/Antigen Arrays | Antibodies/Antigens immobilized onto the solid substrates. Targets proteins in samples captured by the antibodies/antigens. | ~ 4000 (antibody arrays)/ up ~ 21,000 (antigen arrays) | ~ 1-64 | Low picogram/ 5 logs | Colorimetric assays or fluorescence | Targeted | Standardized workflows, Semi-automated | Widely adopted approach with flexible experimental design and PTM profiling. | Limit on inter-assay reproducibility and quantification, inter-assay variation, Sample labelling |
Aptamer-based Assay | Short single-strand DNA or RNA fold into specific tertiary structures with the ability to bind targets with high affinity and specificity. | ~ 7000 | Up to 1000 | Low picogram/ 4-5 logs | DNA microarray/ fluorescence | Targeted | Standardized workflows performed at service centers, Semi-automated | High-plexity | Limit on protein PTMs detection; Dependence on DNA microarray for readout |
Proximity extension assay (PEA) | Sandwich ELISA labeled with complementary DNA oligos binds to the target allowing the oligos to hybridized. | ~ 3000 | 88 | Low picogram to femtogram/ 10 logs | qPCR (medium-plex) or NGS (high-plex) | Targeted | Standardized workflows with Semi-automated | Very little sample required with large dynamic ranges | Dependence on Q-PCR/NGS for readout |
Reverse phase protein arrays (RPPA) | Protein samples immobilized onto the solid substrates. Targets detected by antibodies with signal amplification. | ~ 500 | Up to 1056 | Femtogram/ 5-6 logs | Colorimetric assays or fluorescence | Targeted | Heavy instrumentation and non-standardized workflows, Semi-automated | Large scale parallel analysis for samples. Suitable for protein PTMs | Relatively long turnaround time |