title: Drift tube ion mobility and four-dimensional molecular feature extraction enable data-independent tandem mass spectrometric 'omics' analysis without quadrupole selection.
abstract: BACKGROUND
  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.
authors.affiliation: Agilent Technologies, Beijing, 100102, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Ma
authors.affiliation: Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemistry Physics, Chinese Academy of Sciences, Dalian, 116023, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Liu
authors.affiliation: Agilent Technologies, Beijing, 100102, China.
authors.forename: Zhengxiang
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Agilent Technologies, Beijing, 100102, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Bo
authors.affiliation: Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Bai
authors.affiliation: Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
authors.forename: Huwei
authors.initials: H
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid; D011506:Proteins / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D011506:Proteins