Table 1. Comparison of Three Different Data Acquisition Methods Employed in Bottom-Up Proteomics^a.

bottom-up proteomics acquisition methods
data-dependent acquisition (DDA)	quantitative MS/MS	data-independent acquisition (DIA)
data analysis is easy	number of peptides that can be quantified in each injection is limited (10s–100s)	generates highly reproducible data
number of most abundant ions for fragmentation should be defined	data analysis is easy	able to quantify 10000s of peptides
lower reproducibility	generates highly reproducible data	information should be defined including mass range, precursor ion window width and number of MS/MS scans
generates product ion spectra of peptides for either identification or as SWATH-MS ion library	highly specific and sensitive	requires creation of spectral library by DDA
often used as a prerequisite for targeted MS method development	requires optimization of method for target peptides	data analysis and interpretation is more complex with specific software

^aAbbreviations: SWATH - sequential window acquisition of all theoretical fragmentation spectra.