Using Data-Independent Mass Spectrometry to Extend Detectable Dynamic Range without Prior Fractionation - Proteomic and Metabolomic Approaches to Biomarker Discovery - page 122

down to 50 copies/cell and thus similar in sensi-
tivity to reports on the same type yeast samples
using multiple reaction monitoring (MRM) that
were capable of detecting proteins from the
entire dynamic range of yeast protein expression
( Figure 3 ). 22 This attribute of PAcIFIC is mainly
due to the DIA nature of the technique that

conducts CID regardless of the signal intensity
in the selected m/z channel and the ampli

ca-
tion of signal over noise in tandem mass spectra.
Speci cally, one advantage of the DIA PAcIFIC

method is that peptides with low or no precursor
ion signal are not discriminated against as is the
case with DDA methods.

FIGURE 3 Dynamic range achieved by PAcIFIC in yeast. PAcIFIC was applied to a total yeast cell lysate and identified
proteins, with two or more peptides per protein, compared to the quantitative data set published by Weissmann and
colleagues. 21 Frequencies of proteins identi

ed are calculated for several bins corresponding to different abundance ranges
(copies/cell) as measured in the Weissmann data set. A similar trend is observed in terms of protein abundance categories
with proteins identi ed with less than 50 copies per cell, clearly highlighting the dynamic range and sensitivity achieved

by our data-independent PAcIFIC method. nTOT: total number of protein identi ed; nQUANT: total proteins with

quantitative information; exp. problem: de ned by Weissmann et al. as a detected band by Western blot with an exper-

imental quanti cation problem. (Reprinted with permission from reference #16. Copyright 2011 American Chemical Society.)