Dataset Information

Data-dependent and independent acquisition of complex human-Salmonella mixed proteomes

ABSTRACT: Viewing the scarce amount of protein material coming from the bacterial pathogen in infection models and despite the availability of contemporary, highly sensitive and fast scanning mass spectrometers, the power requirement still not suffices to study the host and pathogen proteomes simultaneously. In the present work we aimed to establish a DIA mass spectrometry workflow for improving the protein identification and quantification of LC-MS/MS, particularly in case of complex samples containing a fairly low amount of peptide material derived from Salmonella, therefore enabling simultaneous host and pathogen protein expression profiling reflecting actual infection conditions.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell

SUBMITTER: Ursula Fels

LAB HEAD: Petra Van Damme

PROVIDER: PXD017945 | Pride | 2021-01-28

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	B005217_Bp_uPac3_CMB-480_KRGEV-UrsulaFels-DIA_SL1344_HeLa_ratios-1_9999_S-H-1.raw	Raw
	B005219_Bp_uPac3_CMB-480_KRGEV-UrsulaFels-DIA_SL1344_HeLa_ratios-1_9999_S-H-2.raw	Raw
	B005221_Bp_uPac3_CMB-480_KRGEV-UrsulaFels-DIA_SL1344_HeLa_ratios-1_9999_S-H-3.raw	Raw
	B005223_Bp_uPac3_CMB-480_KRGEV-UrsulaFels-DIA_SL1344_HeLa_ratios-1_999_S-H-2.raw	Raw
	B005225_Bp_uPac3_CMB-480_KRGEV-UrsulaFels-DIA_SL1344_HeLa_ratios-1_999_S-H-3.raw	Raw

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Publications

Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling.

Willems Patrick P Fels Ursula U Staes An A Gevaert Kris K Van Damme Petra P

Journal of proteome research 20210119 2

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 ...[more]

PMID: 33467856

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