In mass spectrometry, data-independent acquisition (DIA) is a method of molecular structure determination in which all ions within a selected '' m/z'' range are fragmented and analyzed in a second stage of

tandem mass spectrometry Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A com ...

. Tandem mass spectra are acquired either by fragmenting all ions that enter the mass spectrometer at a given time (called broadband DIA) or by sequentially isolating and fragmenting ranges of '' m/z''. DIA is an alternative to

data-dependent acquisition Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A com ...

(DDA) where a fixed number of precursor ions are selected and analyzed by

Broadband

One of the first DIA approaches was a nozzle-skimmer dissociation method called shotgun

collision-induced dissociation Collision-induced dissociation (CID), also known as collisionally activated dissociation (CAD), is a mass spectrometry technique to induce fragmentation of selected ions in the gas phase. The selected ions (typically molecular ions or protonate ...

(CID). Fragmentation can be in the

ion source An ion source is a device that creates atomic and molecular ions. Ion sources are used to form ions for mass spectrometers, optical emission spectrometers, particle accelerators, ion implanters and ion engines. Electron ionization Electron ...

of the mass spectrometer by increasing the nozzle-skimmer voltage in

electrospray ionization Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules becaus ...

. MS^E is a broadband DIA technique that uses alternating low-energy CID and high-energy CID. The low-energy CID is used to acquire precursor ion

mass spectra A mass spectrum is a histogram plot of intensity vs. ''mass-to-charge ratio'' (''m/z'') in a chemical sample, usually acquired using an instrument called a ''mass spectrometer''. Not all mass spectra of a given substance are the same; for example ...

whereas the high-energy CID is used to obtain product ion information by tandem mass spectrometry.

Data analysis

Data analysis is generally challenging for DIA methods as the resulting fragment ion spectra are highly multiplexed. In DIA spectra therefore the direct relation between a precursor ion and its fragment ions is lost since the fragment ions in DIA spectra may potentially result from multiple precursor ions (any precursor ion present in the m/z range from which the DIA spectrum was derived). One approach to DIA data analysis attempts to use database-based search engines used in data-dependent acquisition to search the produced multiplexed spectra. This approach can be improved by assigning individual fragment ion to precursor ions observed in precursor ion scans, using the elution profile of the fragment ions and the precursor ions, and then searching the resulting "pseudo-spectra". A second approach to DIA data analysis is based on a targeted analysis, also known as SWATH-MS (Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra). This approach uses targeted extraction of fragment ion traces directly for identification and quantification without an explicit attempt to de-multiplex the DIA fragment ion spectra.

Broadband

Data analysis

See also

References

Further reading