Table 3 Advantages and limitations of MS and NMR spectroscopy as an analytical tool in profiling of endophytic-derived metabolites

Sensitivity

High sensitivity and lower detection limits (reaching nanomolar). Endophytic metabolites with nanomolar concentrations are readily detected

Low but can be enhanced with higher magnetic field strength, multiple scans, cryo- and microprobes and hyperpolarization

(Mompean et al., 2018; Donnelly et al. 2019; Emwas et al. 2019; Liu et al. 2021a, b)

Sample measurement

Different ionization methods are implemented to increase the coverage of detected metabolites

All metabolites at a detectable concentration level can be quantified in one measurement

(Yoon et al., 2013; Emwas et al. 2019)

Reproducibility

Average reproducibility

Very high. This is one of the key advantages in NMR spectroscopy

(Emwas et al. 2019; Liu et al. 2021a, b)

Selectivity

Selective, and is a superior tool for targeted analysis when in combination with liquid or gas chromatography

NMR is generally used for nonselective analysis

(Emwas et al. 2019; Liu et al. 2021a, b; Mal et al. 2021; Snow 2021)

Sample preparation

Complex sample preparation required; different columns and optimization of ionization conditions; coupled with chromatography and sample derivatizations for GC–MS is required

Minimal sample preparation

(Emwas et al. 2019; Liu et al. 2021a, b; Mal et al. 2021)

Target analysis

Superior for targeted analysis

It is not ideal for targeted analysis

(Vidova and Spacil 2017; Bingol 2018)

Sample recovery

Destructive technique, sample cannot be recovered after analysis, although, relatively small amount is needed

It is nondestructive, allowing multiple analysis on one sample, and sample can be recovered and stored for long periods

(Emwas et al. 2019; Kumar et al. 2019; Mulder et al. 2023)

Sample analysis time

Slower than NMR, as different chromatographic techniques are employed depending on the metabolite

Fast-the entire sample can be analysed in one measurement

(Yoon et al., 2013; Emwas et al. 2019)

Quantitative analysis

The intensity of the MS signal frequently lacks a direct correlation with metabolite concentrations because ionization efficiency exerts a substantial influence

NMR possesses an inherent quantitative nature since the signal intensity correlates directly with metabolites concentration and the number of nuclei present in the molecule

(Yoon et al., 2013; Simmler et al. 2014; Emwas et al. 2019; Liu et al. 2021a, b)

Number of detectable metabolites

300 to over 1000, depending on the MS coupling used

30 to 100. Depending on spectral resolution, usually less than 200 metabolites can be clearly detected and identified in a single measurement

(Yoon et al., 2013; Emwas et al. 2019)

Cost

Cheaper and occupies less space compared to NMR facilities

Higher sample cost

More expensive and occupies more space than MS

Low cost per sample

(Yoon et al., 2013)