The DIA method, or the origin of the SWATH-MS approach, was initially developed in a fast scanning LTQ linear ion trap mass spectrometer.[77,78] However, this method has also been used in LTQ-Orbitrap, for example, using electron transfer dissociation with supplemental activation (ETCaD). Both of the cited works were conducted independently from the manufacturer. In the study that used a LTQ linear ion trap mass spectrometer, the system was set to sequentially isolate and fragment precursor windows of 10 Th (in the ion trap) by collision-activated dissociation (CAD) until a desired range was covered. It was shown that there was a three to fivefold improvement in the signal-to-noise ratio of the ion chromatograms in comparison to DDA. Furthermore, the method provided time-consistent ion sampling and was able to identify peptides undetected in MS1. The increased sensitivity is due to the ability of the linear ion trap to accumulate selected precursor ions for MS2, thereby becoming less affected by chemical noise than MS1. Automatic gain control (AGC) on ion-trap mass spectrometers further improves the detection of low abundance molecular species. Although the precursor window is smaller than that in SWATH-MS approach, equally, the lack of precise knowledge of the peptide precursor ion and the overlapping of spectra owning to co-elution of peptides do cause problems in standard peptide identification programs, though effort has been made to develop software program to deconvolute complex DIA or multiplexed spectra. A program named XDIA Processor from Yates's laboratory has been made available to pre-process the DIA spectra acquired on Orbitrap mass spectrometers prior to database searching.
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