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Anal Bioanal Chem. 2016 Jul;408(18):5031-40. doi: 10.1007/s00216-016-9607-8. Epub 2016 May 17.

Nested data independent MS/MS acquisition.

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Kantonales Labor Zürich, Official Food Control Authority, Fehrenstrasse 15, 8032, Zürich, Switzerland.
Kantonales Labor Zürich, Official Food Control Authority, Fehrenstrasse 15, 8032, Zürich, Switzerland.


Data independent acquisition (DIA) attempts to provide comprehensive MS/MS data while providing a cycle time that is capable of following the elution profile of chromatographic peaks. Currently available MS technology is not yet fully capable of fulfilling these expectations. This paper suggests a new multiplex-based approach to more closely achieve this objective. Customized scans have been programmed for a Q Orbitrap instrument. Multiple nonadjacent mass range segments are sequentially collected (cut out) by the quadrupole. These combined mass ranges undergo fragmentation, and the resulting product ions are analyzed as a whole by the Orbitrap analyzer. The systematical variation of the mass range segments (nested design) permits the mathematical assignment of the observed product ions within a narrow precursor mass range. The proposed approach allows the use of mass windows that are narrower than those in conventional DIA (SWATH). A unique aspect of the proposed approach is the fact that halving the mass window width requires the addition of only a single multiplexed scan. This is different from conventional DIA, which requires the number of mass windows to be doubled in order to achieve the same objective. This paper shows that for a given cycle time, the proposed nested DIA technique produces significantly less chimeric product ion spectra than conventional DIA. However, further improvements from the programming, and most likely the hardware side, are still required in order to achieve the aim of comprehensive MS/MS. Graphical Abstract Schematic of nested design.


Comprehensive MS/MS; Data independent acquisition; Mass spectrometry; Orbitrap


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