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Factorial Experimental Designs Elucidate Significant Variables Affecting Data Acquisition on a Quadrupole Orbitrap Mass Spectrometer

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Journal of The American Society for Mass Spectrometry

Abstract

Instrument parameter values for a quadrupole Orbitrap mass spectrometer were optimized for performing global proteomic analyses. Fourteen factors were evaluated for their influence on data-dependent acquisition with an emphasis on both the rate of sequencing and spectral quality by maximizing two individually tested response variables (unique peptides and protein groups). Of the 14 factors, 12 factors were assigned significant contrast values (P < 0.05) for both response variables. Fundamentally, when optimizing parameters, a balance between spectral quality and duty cycle needs to be reached in order to maximize proteome coverage. This is especially true when using a data-dependent approach for sequencing complex proteomes. For example, maximum ion injection time, automatic gain control settings, and minimum threshold settings for triggering MS/MS isolation and activation all heavily influence ion signal, the number of spectra collected, and spectral quality. To better assess the effect these parameters have on data acquisition, all MS/MS data were parsed according to ion abundance by calculating the percent of the AGC target reached for each MS/MS event and then compared with successful peptide-spectrum matches. This proved to be an effective approach for understanding the effect of ion abundance on successful peptide-spectrum matches and establishing minimum ion abundance thresholds for triggering MS/MS isolation and activation.

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Acknowledgments

The authors acknowledge Benjamin Orsburn for assisting with the data processing. The authors gratefully acknowledge funding support from NSF Grant CBET-0966859, the W. M. Keck Foundation, and North Carolina State University.

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Authors and Affiliations

  1. W. M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA

    Shan M. Randall & David C. Muddiman

  2. Thermo Fisher Scientific, San Jose, CA, 95134, USA

    Helene L. Cardasis

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  1. Shan M. Randall
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  2. Helene L. Cardasis
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  3. David C. Muddiman
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Correspondence to David C. Muddiman.

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Randall, S.M., Cardasis, H.L. & Muddiman, D.C. Factorial Experimental Designs Elucidate Significant Variables Affecting Data Acquisition on a Quadrupole Orbitrap Mass Spectrometer. J. Am. Soc. Mass Spectrom. 24, 1501–1512 (2013). https://doi.org/10.1007/s13361-013-0693-y

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  • DOI: https://doi.org/10.1007/s13361-013-0693-y

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