Using Data-Independent Mass Spectrometry to Extend Detectable Dynamic Range without Prior Fractionation - Proteomic and Metabolomic Approaches to Biomarker Discovery - page 117

method of acquiring tandem mass spectrometry
as

Principle of the Precursor Acquisition
Independent from Ion Count (PAcIFIC)
The data-independent acquisition (DIA)
method described here acquires tandem mass
spectra at every m/z value (i.e., at each m/z
“

precursor acquisition independent from ion
count

“

” (PAcIFIC), which in our rst report

worked as follows. 12 During a

first injection, the
ion trap is used toperformdata-independent colli-
sion-induced dissociation (CID) at each of 10
contiguous 1.5 m/z intervals across a range of 15
m/z per LC-MS analysis ( Figure 1 A) using a 2.5
m/z isolationwidth. In the next LC-MS/MS anal-
ysis a new 15 m/z range is examined in an iden-
tical

) without regard to whether a precur-
sor ion is observed. This nonstochastic approach
does not require precursor ion scans, but they
can be added in using certain hybrid MS con

channel ”

gu-
rations. We therefore refer to the following DIA fashion and so on until the considered

FIGURE 1 Principle of PAcIFIC. With this method, the sample is repeatedly analyzed by LC-MS/MS. (A) During each
injection, a different precursor-ion m/z range is selected for tandem mass spectrometry independent of the precursor ion
measurement. (B) In each narrow m/z range, all precursor ions are isolated in the ion trap and subjected to collision induced
dissociation until the desired m/z range is achieved. (C) Each spectra is then searched against a database using the center of
the window as the precursor mass and a tolerance corresponding to maximum charge state allowed times the isolation width
divided by 2, such as 3(2.5/2) 3.75 Da. (Reprinted with permission from reference #12. Copyright 2009 American Chemical

¼

Society.)