Use of hybrid data-dependent and -independent acquisition spectral libraries empowers dual-proteome profiling
- Author
- Patrick Willems (UGent) , Ursula Fels, An Staes (UGent) , Kris Gevaert (UGent) and Petra Van Damme (UGent)
- Organization
- Project
-
- PROPHECY (PROPHECY: Translational control in infection biology: riboproteogenomics of bacterial pathogens)
- Riboproteogenomics of the sORF-encoded Salmonella peptidome
- 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: http://hdl.handle.net/1854/LU-8688450
- 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://doi.org/10.1021/acs.jproteome.0c00350}},
volume = {{20}},
year = {{2021}},
}
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