Table 1.
Overview of proteomics, LC-MS based metabolomics, and lipidomics platforms.
| Aim of the Analysis | Proteomics | Proteomics | Proteomics | Metabolomics | Lipidomics |
|---|---|---|---|---|---|
| Platform | Mass spectrometry | Proximity Extension Assay (Olink) | Aptamer-based platform (SomaScan) | Mass spectrometry | Mass spectrometry |
| Analytes | Proteins | Proteins | Proteins | Polar small molecules (below 1500 Da), including carbohydrates, ketones, aminoacids andbiogenic amides | Apolar molecules, including glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, polyketides, sterol and prenol lipids [47] |
| Analyte separation | Liquid chromatography | No | No | Liquid chromatography | Liquid chromatography (no for direct infusion) |
| Analysis of body fluids (e.g., plasma, serum, urine, saliva) | Yes | Yes | Yes | Yes | Yes |
| Analysis of tissue/cell culture | Yes | Not optimal | Not optimal | Yes | Yes |
| Analysis of proteoforms (PTMs, isoforms, coding-variants) | Yes | No | No | Not applicable | Not applicable |
| Analyte multi-plexing | Varies depending on the workflow and specimen, up to >10,000 proteins [29,81] (300–5000 in plasma) [33,35,36] | 1472 proteins (targeted panels of 48–384 proteins) a | 7000 proteins b | Varies depending on the workflow and specimen [82] (expected up to 10% of molecular features identification) [83] | Varies depending on the workflow and specimen [82], currently up to 1108 lipids in plasma [64] |
| Dynamic range | High-medium abundance in case of plasma | (pg/mL to µg/mL) c | (femtomolar to micromolar) d | (picomolar to milimolar) [42,84] | (picomolar to nanomolar) [85] |
| Reproducibility | Medium | Medium to High (Intra-assay CV 10–12% for the 384-protein panels) e |
High (Median intra-assay CV 4.6% for the 1300-protein platform) f |
Medium to high [83,86] | Medium to high [86] |
| Throughput (per day per system) | Low to medium (10 s–100 s) | High (100 s) | High (100 s) | Medium to high (10 s–100 s) | Medium to high (10 s–100 s) |
| Quantification | Relative or absolute for targeted assays | Relative or absolute for targeted assays | Relative | Relative or absolute for targeted assays | Relative or absolute for targeted assays |
ahttps://www.olink.com/products/olink-explore/; bhttps://somalogic.com/life-sciences/; chttps://www.olink.com/content/uploads/2017/02/1068-v1.0-Proseek-Multiplex-Development-Validation-data_final.pdf; dhttps://somalogic.com/dynamic-range/; ehttps://www.olink.com/content/uploads/2021/03/Explore_Demo_Certificate-of-Analysis_2021-03-30.pdf; fhttps://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf. All the above webpages were last accessed on 1 October 2021.