TABLE 1:

Comparison of MS-based proteomics methods.

	Shotgun	SRM	Data-independent acquisition (SWATH-MS)
Throughput	High	Low to medium	Medium to high
Reproducibility	Low	High	High
Identification specificity	High	Medium	Medium
Sensitivity	Low to medium	High to very high	Medium to high
Quantitative accuracy	Medium to high	High to very high	High
Acquisition method	Fragment spectra	Fragment chromatograms	Fragment spectra and chromatograms
Application	Protein enumeration and discovery	Reproducible quantification	Reproducible quantification in high throughput
Analysis software	Well established	Visual (manual)	Multiple tools available

This table compares three major techniques used in mass spectrometry–based proteomics according to different performance criteria: shotgun proteomics, targeted proteomics or SRM, and data-independent acquisition or SWATH-MS. All three techniques have unique benefits and disadvantages; therefore different techniques need to be applied for different tasks.