Table 5 Overview of proteomic platforms used for biomarker development
Category | Platform | Multiplex capability | Application | LOD | Advantages | Limitations |
|---|---|---|---|---|---|---|
Antibody-Based | ELISA | 96 proteins per assay | Biomarker evaluation & validation | pg/mL | Highly sensitive for protein(s) of interest | Dependant on antibody availability Influenced by non-standardised variables e.g. temperature, pH, antibodes used Large amounts of protein lysate required |
Protein microarrays |  > 1000 proteins per screen | Biomarker evaluation & validation Biomarker discovery | pg/mL | High throughput for multiplexed analysis | Reliant on availability of antibodies Expensive Biased to pre-selected proteins if used for biomarker discovery Two antibodies required per protein | |
Proximity extension assay (PEA) | Up to 100 proteins per array | Biomarker discovery | pg/mL | High throughput Highly sensitive for proteins of interest | Expensive Biased to pre-selected proteins if used for biomarker discovery Two antibodies required per protein | |
Aptamer-based | Somascan | Up to 2000 proteins per screen | Biomarker evaluation & validation Biomarker discovery | fg/mL | Aptamers cheaper to produce More sensitive than antibody-based techniques Aptamers available for wider range of molecules High throughput Minimal sample required | Biased to pre-selected proteins if used for biomarker discovery |
Mass Spectrometry-based | DDA e.g. LC–MS/MS | 1000′s of proteins | Biomarker discovery | ng/mL | High throughput Minimal sample required Unbiased screen of all detectable proteins No requirement for antibodies or somamers | Complex sample preparation required Enrichment techniques required to detect very low abundant proteins in clinical samples |
DIA e.g. SWATH & DIA PASEF | 1000′s of proteins | Biomarker discovery | ng/mL | High throughput Minimal sample required Unbiased screen of all detectable proteins No requirement for antibodies or somamers Increased coverage of sample proteome Has been optimised for analysis of complex sample types such as FFPE tissue | Complex sample preparation required Enrichment techniques required to detect very low abundant proteins in clinical samples Requires specialised Mass Spectrometer Data storage | |
MRM | Up to 100 proteins per run | Biomarker evaluation & validation | ng/mL | Highly selective for proteins of interest High throughput No requirement for antibodies/somamers Wide dynamic range | Complex sample preparation required Can be affected by interfering signal from complex biological samples Labour intensive method development | |
PRM |  > 100 proteins per run | Biomarker evaluation & validation Biomarker discovery | ng/mL | Greater sensitivity than MRM Interfering signals filtered out Method development less labour intensive than MRM | Complex sample preparation required Measurements not as precise as MRM Higher LOQ than MRM |