Table 1.

Current Scale, Strengths, and Challenges of MS-based Metabolomics and MS-based Proteomics.

Metabolomics	Proteomics
Scale
> 40,000 annotated human metabolites and an estimated > 200,000 possible metabolites Highly diverse structural forms and high number of isomers Highly diverse physiochemical properties	> 20,000 base human proteins and an estimated > 1,000,000 possible protein variants Predominantly linear polymers and high number of isomers Highly diverse physiochemical properties
Strengths
Many metabolites are common across species; experimental evidence can be shared to guide identifications Metabolic state dynamics is relatively fast Sample preparation can be relatively simple (i.e.,. lysis and extraction) or more complex (i.e., added steps of purification an fractionation) depending on goals of the experiment	False discovery rates can be estimated Protein identification can be inferred from unique fragments (i.e. peptides) comprising the protein Fragmentation patterns are relatively predictable Standard reference proteins are not requiredfor protein assignments Many proteins are species specific; it may bepossible to discern biological source in a microbiome study
Challenges
False discovery rates are difficult to ascertain There is a lack of standard reference material for many metabolites Metabolite identification cannot be inferred from fragments comprising the whole metabolite Fragmentation patterns are relatively unpredictable or uninformative (similar fragments for different species) Many metabolites are common across species; it is challenging to discern the source in microbiome study	Protein expression profile dynamics is relatively slow Sample preparation is often multi-step (e.g. lysis, purification, enzymatic digestion, and solid phase extraction) depending on goals of the experiment