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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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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Project description:Host-pathogen interactions result in complex relationship, many aspects of which are not completely understood. Vip proteins, which are Bacillus thuringensis (Bt) insecticidal toxins produced during the vegetative stage, are selectively effective against specific insect pests. This new group of Bt proteins represents an interesting alternative to the classical Bt Cry toxins because current data suggests that they do not share the same mode of action. We have designed and developed a genome-wide microarray for the beet armyworm Spodoptera exigua, a serious lepidopteran pest of many agricultural crops, and used it to better understand how Lepidopteran larvae respond to the treatment with the insecticidal protein Vip3Aa. With this approach, the goal of our study was to evaluate the changes in gene expression levels caused by treatment with sublethal doses (causing 99% growth inhibition) of Vip3Aa at 8 and 24 h after treatment. Results indicated that the toxin provoked a wide transcriptional response, with 19% of unigenes in the microarray responding significantly to treatment. The number of up- and down-regulated unigenes was very similar.. The number of genes whose expression was regulated at 8 h was similar to the number of genes whose expression was regulated after 24 h of treatment. The up-regulated sequences were enriched for genes involved in innate immune response and in pathogen response such as antimicrobial peptides (AMPs) and repat genes. The down-regulated sequences were mainly unigenes with homology to genes involved in metabolism. Genes related to the mode of action of Bt Cry proteins were found, in general, to be slightly overexpressed. The present study is the first genome-wide analysis of the response of lepidopteran insects to Vip3Aa intoxication. An insight into the molecular mechanisms and components related to Vip intoxication will allow designing of more effective management strategies for pest control. Changes in gene expression levels caused by treatment with sublethal doses (causing 99% growth inhibition) of Vip3Aa were measured at 8 and 24 h after treatment by means of custom Spodoptera exigua microarray. Six to seven larvae were used for each time point and three independent experiments were performed at each time point.

Dataset Information

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

Publications

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

Similar Datasets

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