Discovery-based Quantitative MS methods,(“shotgun” proteomics), aim to identify as many proteins in a sample as possible and can be completed on a wide range of samples with minimal method development.
- DDA (data-dependent acquisition): In Data-dependent acquisition (DDA) mode a MS instrument will complete a full scan of all peptide (precursor) ions during MS1 and then select the most abundant ions for fragmentation and MS2
- DIA (data-independent acquisition): In Data-independent acquisition (DIA) mode a MS instrument
scans pre-determined, often sequential, m/z ranges and then fragments all the ions within each range for MS2 measurement
DDA
DIA
Suitable for small proteomes*
Yes
Yes
Suitable for large proteomes*
No
Yes
Dynamic range
Moderate
High
Complexity of spectra
Low
High
Search requirements
Protein database
Spectral library
Instrument method optimization
Low
Hig
Note (*) Most prokaryote proteomes can be considered a “small” proteome, vs. larger eukaryotic or mixed (e.g., infection model) proteomes
Discovery-based methods can be used to identify thousands of proteins in a single sample, and for most research questions label-free DDA is a straight-forward option that has relatively low reagents costs, and requires minimal sample preparation and instrument method optimization.
Discovery-based Quantitative MS methods
Quantitative Proteomics to Label or not to Label