Table 1.

Comparison of metabolomics and proteomics technologies for circulating biomarker discovery

	Metabolomics	Proteomics
Analytes Measured	Circulating small molecules	Circulating proteins
Technologies	1. NMR 2. MS  a. GC-MS  b. LC-MS	1. MS 2. Multiplex-nucleic acid affinity reagents (aptamers) 3. PEA with nucleotide-labeled antibodies
Strengths	1. Technologies are high-throughput 2. High sensitivity and specificity 3. NMR is sample non-destructive 4. Small sample amount needed 5. Unbiased measurement of unknown compounds are possible	1. Most technologies are high-throughput 2. Relatively good sensitivity and specificity 3. Small sample amount needed 4. Proteins are direct products of transcription, facilitating integration with genomic data
Limitations	1. Identification of unknown compounds is labor intensive 2. Metabolite pathway analysis is complex	1. High-throughput methods may have slightly lower specificity 2. Limited ability to identify unknown proteins

NMR: nuclear magnetic resonance, MS: mass spectrometry, GC: gas chromatography, LC: liquid chromatography, PEA: proximity extension assay