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Use of hybrid data-dependent and -independent acquisition spectral libraries empowers dual-proteome profiling

Patrick Willems (UGent) , Ursula Fels (UGent) , An Staes (UGent) , Kris Gevaert (UGent) and Petra Van Damme (UGent)
(2021) JOURNAL OF PROTEOME RESEARCH. 20(2). p.1165-1177
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Abstract
In the context of bacterial infections, it is imperative that physiological responses can be studied in an integrated manner, meaning a simultaneous analysis of both the host and the pathogen responses. To improve the sensitivity of detection, data-independent acquisition (DIA)-based proteomics was found to outperform data-dependent acquisition (DDA) workflows in identifying and quantifying low-abundant proteins. Here, by making use of representative bacterial pathogen/host proteome samples, we report an optimized hybrid library generation workflow for DIA mass spectrometry relying on the use of data-dependent and in silico-predicted spectral libraries. When compared to searching DDA experiment-specific libraries only, the use of hybrid libraries significantly improved peptide detection to an extent suggesting that infection-relevant host-pathogen conditions could be profiled in sufficient depth without the need of a priori bacterial pathogen enrichment when studying the bacterial proteome. Proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD017904 and PXD017945.
Keywords
Biochemistry, General Chemistry, bacterial pathogen/host interaction, data-dependent acquisition (DDA), data-independent acquisition (DIA), Salmonella, spectral library, PEPTIDE IDENTIFICATION, SOFTWARE TOOLS, QUANTIFICATION, TYPHIMURIUM, (MSPIP)-P-2, PROTEINS, RATES

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Citation

Please use this url to cite or link to this publication:

MLA
Willems, Patrick, et al. “Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling.” JOURNAL OF PROTEOME RESEARCH, vol. 20, no. 2, 2021, pp. 1165–77, doi:10.1021/acs.jproteome.0c00350.
APA
Willems, P., Fels, U., Staes, A., Gevaert, K., & Van Damme, P. (2021). Use of hybrid data-dependent and -independent acquisition spectral libraries empowers dual-proteome profiling. JOURNAL OF PROTEOME RESEARCH, 20(2), 1165–1177. https://doi.org/10.1021/acs.jproteome.0c00350
Chicago author-date
Willems, Patrick, Ursula Fels, An Staes, Kris Gevaert, and Petra Van Damme. 2021. “Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling.” JOURNAL OF PROTEOME RESEARCH 20 (2): 1165–77. https://doi.org/10.1021/acs.jproteome.0c00350.
Chicago author-date (all authors)
Willems, Patrick, Ursula Fels, An Staes, Kris Gevaert, and Petra Van Damme. 2021. “Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling.” JOURNAL OF PROTEOME RESEARCH 20 (2): 1165–1177. doi:10.1021/acs.jproteome.0c00350.
Vancouver
1.
Willems P, Fels U, Staes A, Gevaert K, Van Damme P. Use of hybrid data-dependent and -independent acquisition spectral libraries empowers dual-proteome profiling. JOURNAL OF PROTEOME RESEARCH. 2021;20(2):1165–77.
IEEE
[1]
P. Willems, U. Fels, A. Staes, K. Gevaert, and P. Van Damme, “Use of hybrid data-dependent and -independent acquisition spectral libraries empowers dual-proteome profiling,” JOURNAL OF PROTEOME RESEARCH, vol. 20, no. 2, pp. 1165–1177, 2021.
@article{8688450,
  abstract     = {{In the context of bacterial infections, it is imperative that physiological responses can be studied in an integrated manner, meaning a simultaneous analysis of both the host and the pathogen responses. To improve the sensitivity of detection, data-independent acquisition (DIA)-based proteomics was found to outperform data-dependent acquisition (DDA) workflows in identifying and quantifying low-abundant proteins. Here, by making use of representative bacterial pathogen/host proteome samples, we report an optimized hybrid library generation workflow for DIA mass spectrometry relying on the use of data-dependent and in silico-predicted spectral libraries. When compared to searching DDA experiment-specific libraries only, the use of hybrid libraries significantly improved peptide detection to an extent suggesting that infection-relevant host-pathogen conditions could be profiled in sufficient depth without the need of a priori bacterial pathogen enrichment when studying the bacterial proteome. Proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD017904 and PXD017945.}},
  author       = {{Willems, Patrick and Fels, Ursula and Staes, An and Gevaert, Kris and Van Damme, Petra}},
  issn         = {{1535-3893}},
  journal      = {{JOURNAL OF PROTEOME RESEARCH}},
  keywords     = {{Biochemistry,General Chemistry,bacterial pathogen/host interaction,data-dependent acquisition (DDA),data-independent acquisition (DIA),Salmonella,spectral library,PEPTIDE IDENTIFICATION,SOFTWARE TOOLS,QUANTIFICATION,TYPHIMURIUM,(MSPIP)-P-2,PROTEINS,RATES}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{1165--1177}},
  title        = {{Use of hybrid data-dependent and -independent acquisition spectral libraries empowers dual-proteome profiling}},
  url          = {{http://dx.doi.org/10.1021/acs.jproteome.0c00350}},
  volume       = {{20}},
  year         = {{2021}},
}

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