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Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization.

Publication ,  Journal Article
Moseley, MA; Hughes, CJ; Juvvadi, PR; Soderblom, EJ; Lennon, S; Perkins, SR; Thompson, JW; Steinbach, WJ; Geromanos, SJ; Wildgoose, J ...
Published in: J Proteome Res
February 2, 2018

A novel data-independent acquisition (DIA) method incorporating a scanning quadrupole in front of a collision cell and orthogonal acceleration time-of-flight mass analyzer is described. The method has been characterized for the qualitative and quantitative label-free proteomic analysis of complex biological samples. The principle of the scanning quadrupole DIA method is discussed, and analytical instrument characteristics, such as the quadrupole transmission width, scan/integration time, and chromatographic separation, have been optimized in relation to sample complexity for a number of different model proteomes of varying complexity and dynamic range including human plasma, cell lines, and bacteria. In addition, the technological merits over existing DIA approaches are described and contrasted. The qualitative and semiquantitative performance of the method is illustrated for the analysis of relatively simple protein digest mixtures and a well-characterized human cell line sample using untargeted and targeted search strategies. Finally, the results from a human cell line were compared against publicly available data that used similar chromatographic conditions but were acquired with DDA technology and alternative mass analyzer systems. Qualitative comparison showed excellent concordance of results with >90% overlap of the detected proteins.

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Published In

J Proteome Res

DOI

EISSN

1535-3907

Publication Date

February 2, 2018

Volume

17

Issue

2

Start / End Page

770 / 779

Location

United States

Related Subject Headings

  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Proteomics
  • Proteome
  • Proteolysis
  • K562 Cells
  • Humans
  • Hela Cells
  • HeLa Cells
  • Escherichia coli
  • Complex Mixtures
 

Citation

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Moseley, M. A., Hughes, C. J., Juvvadi, P. R., Soderblom, E. J., Lennon, S., Perkins, S. R., … Vissers, J. P. C. (2018). Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization. J Proteome Res, 17(2), 770–779. https://doi.org/10.1021/acs.jproteome.7b00464
Moseley, M Arthur, Christopher J. Hughes, Praveen R. Juvvadi, Erik J. Soderblom, Sarah Lennon, Simon R. Perkins, J Will Thompson, et al. “Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization.J Proteome Res 17, no. 2 (February 2, 2018): 770–79. https://doi.org/10.1021/acs.jproteome.7b00464.
Moseley MA, Hughes CJ, Juvvadi PR, Soderblom EJ, Lennon S, Perkins SR, et al. Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization. J Proteome Res. 2018 Feb 2;17(2):770–9.
Moseley, M. Arthur, et al. “Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization.J Proteome Res, vol. 17, no. 2, Feb. 2018, pp. 770–79. Pubmed, doi:10.1021/acs.jproteome.7b00464.
Moseley MA, Hughes CJ, Juvvadi PR, Soderblom EJ, Lennon S, Perkins SR, Thompson JW, Steinbach WJ, Geromanos SJ, Wildgoose J, Langridge JI, Richardson K, Vissers JPC. Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization. J Proteome Res. 2018 Feb 2;17(2):770–779.
Journal cover image

Published In

J Proteome Res

DOI

EISSN

1535-3907

Publication Date

February 2, 2018

Volume

17

Issue

2

Start / End Page

770 / 779

Location

United States

Related Subject Headings

  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Proteomics
  • Proteome
  • Proteolysis
  • K562 Cells
  • Humans
  • Hela Cells
  • HeLa Cells
  • Escherichia coli
  • Complex Mixtures