Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements


Applying Hadamard transform multiplexing to ion mobility separations (IMS) can significantly improve the signal-to-noise ratio and throughput for IMS coupled mass spectrometry (MS) measurements by increasing the ion utilization efficiency. However, it has been determined that fluctuations in ion intensity as well as spatial shifts in the multiplexed data lower the signal-to-noise ratios and appear as noise in downstream processing of the data. To address this problem, we have developed a novel algorithm that discovers and eliminates data artifacts. The algorithm employs an analytical approach to identify and remove artifacts from the data, decreasing the likelihood of false identifications in subsequent data processing. Following application of the algorithm, IMS-MS measurement sensitivity is greatly increased and artifacts that previously limited the utility of applying the Hadamard transform to IMS are avoided.

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The authors thank Richard Zare, Craig Aspinwall, Facundo Fernandez, and Ignacio Zuleta for valuable correspondence and Hadamard transformed data utilizing a large number of bits. S.A.P. was sponsored by the US Department of Energy Science Undergraduate Laboratory Internships (SULI) program. S.H.P. acknowledges funding from a US Department of Energy Early Career award. The development of the IMS-MS platform was provided through the National Institute of Health General Medical Sciences Proteomic Center at PNNL (2 P41 GM 103493-11), and other portions of this research were supported by grants from the National Institute of General Medical Sciences (8 P41 GM103493-10 and R21 GM103497), National Cancer Institute (R21-CA12619-01, U24-CA-160019-01, and Interagency Agreement Y01-CN-05013-29), National Institute of Environmental Health Sciences of the National Institutes of Health (R01ES022190), the Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory and by the US Department of Energy Office of Biological and Environmental Research Genome Sciences Program under the Pan-omics project. Work was performed in the Environmental Molecular Science Laboratory, a US Department of Energy (DOE) national scientific user facility at Pacific Northwest National Laboratory (PNNL) in Richland, WA. Battelle operates PNNL for the DOE under contract DE-AC05-76RLO01830.

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Correspondence to Samuel H. Payne.

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Spencer A. Prost and Kevin L. Crowell contributed equally to this work.

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Prost, S.A., Crowell, K.L., Baker, E.S. et al. Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements. J. Am. Soc. Mass Spectrom. 25, 2020–2027 (2014).

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Key words

  • Ion mobility
  • Computational proteomics
  • Hadamard transform
  • Bioinformatics
  • Sensitivity
  • Data analysis