Dataset Information

Method testing for plasma proteomics

ABSTRACT: We have compared the plasma proteome coverage obtained by using different methods for samplepreparation

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Maria Hernandez-Valladares

LAB HEAD: Maria Hernandez Valladares

PROVIDER: PXD057402 | Pride | 2026-06-29

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	SOL2024021a-10_S2-A11_1_976_DEPL-SP3_5.d.zip	Other
	SOL2024021a-11_S2-A12_1_9724_SP3_1.d.zip	Other
	SOL2024021a-12_S2-B1_1_9786_SP3_2.d.zip	Other
	SOL2024021a-13_S2-B2_1_9719_SP3_3.d.zip	Other
	SOL2024021a-14_S2-B4_1_9697_SP3_4.d.zip	Other

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Publications

Identification of diagnostic biomarkers for relapsing-remitting multiple sclerosis in plasma by mass spectrometry-based proteomics.

García-Silva Víctor M VM Chicano-Galvez Eduardo E García-Sánchez María Isabel MI Peralbo-Molina Ángela Á Hernández-Valladares María M

Journal of neuropathology and experimental neurology 20260701 7

In the absence of molecular biomarkers, the current diagnosis of multiple sclerosis is based on clinical assessment, neuroimaging, and detection of oligoclonal bands in cerebrospinal fluid. Early and rapid diagnosis using patient samples obtained by non-invasive methods would be a major advance in clinical management. We tested 5 different methods for preparation of the plasma proteome for liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis. These were as follows: (1) single- ...[more]

PMID: 41423876

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Project description:Treatment failures of antibiotic therapy are of major concern and can be caused by a misalignment of the antibiotic susceptibility determined in vitro with the behaviour of the pathogen in the patient. The aim of this study was to investigate the transcriptomic response of the uropathogenic strain E. coli CFT073 to antibiotic treatment in blood stream infection (BSI) models in order to understand and avoid antibiotic therapy failures in urosepsis treatments. Blood stream infection models were established by growing E. coli CFT073 in pooled human serum with and without ciprofloxacin and compared to Iso-sensitest medium. The antibiotic challenge was introduced at mid-logarithmic phase of growth of the organism to depict a clinical scenario . Global gene expression profiling of these conditions was examined using commercial DNA microarrays. The organismâs metabolic genes appeared to be regulated differently in each medium, this indicated that the bacterial growth regulation were different between the models. Bacterial growth in human serum mainly involved regulations of amino acid synthesis/utilisation such as glycine, arginine, thiamine, regulations of fimbrial proteins and bacteriophage genes. When comparing the responses to antibiotic challenge, bacteria grown in the respective medium displayed specific responses to the antibiotic challenge which were not seen in the other media. The common functions of genes that responded to the ciprofloxacin challenge were SOS response, DNA repair, DNA replication, fimbrial genes and bacteriophage initiation. A subset of the bacteriophage genes showed similar responses between the three models. From genes that were differentially regulated, responses observed in the serum model appeared to have the highest fold changes. In this study we established new models to investigate blood stream infections. They have been used to identify previously unknown differences in the molecular response to antibiotic treatment by the uropathogenic E. coli CFT073 depending on the media. These unique responses will help to unravel the complexity of bloodstream infection and can help to improve the antibiotic therapy that is used. A 20 array study using total RNA recovered from bacteria from bacteria that were either grown in human serum or Iso-Sensitest (IST) broth, with and without ciprofloxacin challenge. Arrays were performed in 5 biological replicates from each condition.Upon QC checks, certain biological repeats were excluded due to poor hybridisation results.