Drift tube ion mobility and four-dimensional molecular feature extraction enable data-independent tandem mass spectrometric 'omics' analysis without quadrupole selection.

RATIONALE: Quadrupole-based tandem mass spectrometry (MS/MS) plays a critical role in 'omics' studies. However, when a particular m/z precursor is selected by the quadrupole, ions other than the precursor are not transmitted through, and the sensitivity and dynamic range thus diminish. Therefore, separation techniques such as ion mobility (IM) are coupled with MS/MS to improve it.

METHODS: In this workflow, every IM-mass spectrometry (MS) scan was followed by one high-voltage collision energy (CE) scan. The precursors were separated in IM drift time and dissociated after IM; the four-dimensional molecular feature extraction (4D MFE) algorithm was used to align the precursors and their MS/MS spectra based on retention time and drift time distribution. A complicated peptide mixture was selected to exemplify the workflow in a proteomics study.

RESULTS: The new IM-MS-based workflow achieved similar performance in finding proteins compared to the traditional quadrupole-based MS/MS method. However, a significant difference was found between the proteins found by these two methods. For the four concentration levels analyzed, at least 23% more proteins were found by combining the new methods than only using the traditional quadrupole-based MS/MS method.

CONCLUSIONS: The established workflow used the 4D MFE algorithm to analyze a complicated 4D dataset and was demonstrated to find more proteins not found by the traditional quadrupole-based MS/MS method in proteomics application. It is thus an important complementary MS/MS mode for 'omics' studies. Copyright © 2016 John Wiley & Sons, Ltd.