Browse
Submit Data
Databases
API
Help

Dataset Information

183 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mass spectrometry-based clinical proteomic profiling of thrombotic material obtained by endovascular thrombectomy in patients with ischemic stroke

ABSTRACT: Thrombus formation is a dynamic process regulated by flow, blood cells, and plasma proteins. In this study, we have developed a clinical proteomics workflow to characterize the protein cargo of thrombus derived from patients with ischemic stroke.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Enrique SantamarÃa

LAB HEAD: Joaquin Fernandez-Irigoyen

PROVIDER: PXD007666 | Pride | 2018-02-13

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Mass Spectrometry-Based Proteomic Profiling of Thrombotic Material Obtained by Endovascular Thrombectomy in Patients with Ischemic Stroke.

Muñoz Roberto R Santamaría Enrique E Rubio Idoya I Ausín Karina K Ostolaza Aiora A Labarga Alberto A Roldán Miren M Zandio Beatriz B Mayor Sergio S Bermejo Rebeca R Mendigaña Mónica M Herrera María M Aymerich Nuria N Olier Jorge J Gállego Jaime J Mendioroz Maite M Fernández-Irigoyen Joaquín J

International journal of molecular sciences 20180207 2

Thrombotic material retrieved from acute ischemic stroke (AIS) patients represents a valuable source of biological information. In this study, we have developed a clinical proteomics workflow to characterize the protein cargo of thrombi derived from AIS patients. To analyze the thrombus proteome in a large-scale format, we developed a workflow that combines the isolation of thrombus by endovascular thrombectomy and peptide chromatographic fractionation coupled to mass-spectrometry. Using this wo ...[more]

PMID: 29414888

Similar Datasets

Olfactory bulb proteomics in human Alzheimer's disease

Project description:Olfactory dysfunction is among the earliest features of Alzheimer´s disease (AD). Although neuropathological abnormalities have been detected in the olfactory bulb (OB), little is known about its dynamic biology. Here, OB- proteome analysis was performed across different AD stages using a label-free approach.

2018-01-16 | PXD005319 | Pride

Olfactory proteomics in Parkinson disease

Project description:Olfactory dysfunction is one of the earliest features in Lewy-type alpha-synucleinopathies (LTS) such as Parkinson´s disease (PD). However, the underlying molecular mechanisms associated to smell impairment is poorly understood. To reveal the missing links in the biochemical understanding of olfactory dysfunction in PD, we have applied mass spectrometry-based proteomics in postmortem olfactory bulbs (OBs) dissected from parkinsonian subjects with different LTS staging respect to elderly controls (n= 24, mean age 79 years).

2018-10-24 | PXD008036 | Pride

Olfactory bulb proteome characterization in APP/PS1 mice

Project description:Here we used double-transgenic amyloid precursor protein/presenilin 1 (APPswe/PS1dE9) mice and label-free quantitative proteomics to analyze potential early pathological effects on the olfactory bulb (OB) during AD progression.

2016-08-09 | PXD003683 | Pride

Macrophage proteome in response to Mycobacterium tuberculosis infection

Project description:This study investigates the proteomic alterations in human monocytic cell line (THP1) subsequent to infection with different strains of mycobacterium tuberculosis (H37Ra, H37Rv, BND433 and JAL2287) using the SWATH-MS strategy. THP1 proteome was analysed after 6, 18, 30 and 42 hours of infection with each strains and compared to that of uninfected cells. Our findings reveal temporal regulation of host response subsequent to Mtb infection.

2020-09-23 | PXD009046 | Pride

Macrophage proteome in response to Mycobacterium tuberculosis infection

2021-01-05 | PXD022352 | Pride

Differential proteomic analysis by SWATH-MS unravels the most dominant mechanisms underlying yeast adaptation to nonoptimal temperatures under anaerobic conditions- SWATH data

Project description:Elucidation of the mechanism of temperature tolerance in yeast is essential for enhancing cellular robustness of strains, providing more economically and sustainable sound industrial processes. We investigated the differential responses of three distinct Saccharomyces cerevisiae strains, an industrial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and an industrial bioethanol strain, Ethanol Red, grown at sub- (12 ºC) and-supra (39 ºC) optimal temperatures under chemostat conditions, in which specific growth rate–dependent changes are eliminated. In contrast to previous studies, we employed anaerobic conditions, mimicking the industrial processes. The proteomic profile of these strains was performed by SWATH-MS, allowing the quantification of 997 proteins. Our analysis revealed that temperature response differs between the strains, highlighting the precision with which each strain responds to changes in its environment; however, we also found some common responsive proteins among the strains, revealing that the response to temperature involves general stress and specific mechanisms. Overall, sub-optimal temperature conditions involved a higher remodeling of the proteome than supra-optimal temperature. Further, the proteomic data evidenced that the cold response involves a strong repression of translation related proteins as well as induction of amino acid metabolism, together with components related to protein folding and degradation. On the other hand, the high temperature response mainly recruits amino acid metabolism. Our study provides a global and thorough insight into how growth temperature affects yeast proteome, which can be a step forward for research regarding the comprehension and the improvement of yeast thermotolerance.

2021-01-04 | PXD016567 | Pride

Molecular characterization of Histomonas meleagridis exoproteome with emphasis on protease secretion and parasite-bacteria interaction

Project description:Exoproteome from parasitic protists constitutes of extracellular proteins which play a fundamental role in multifactorial host-parasite interactions. Lytic factors, especially secreted proteases in extracellular milieu, are capable to modulate tissue invasion, thereby aggravating host susceptibility. Despite the important role of exoproteins during infection, exoproteomic data on Histomonas meleagridis are non-existent. The present study employed traditional 1D-in-gel-zymography (1D-IGZ) and micro-LC-ESI-MS/MS (shotgun proteomics), to scrutinize H. meleagridis exoproteomes, obtained from a clonal virulent and attenuated strains. Both strains were maintained as mono-eukaryotic monoxenic culture with Escherichia coli. We demonstrated active in vitro secretion kinetics of proteases by both parasites, with widespread proteolytic activity ranging from 17 kDa to 120 kDa. Based on protease inhibitor-susceptibility tests, a predominant repertoire of cysteine proteolysis was present in the parasite exoproteomes, with stronger activity from virulent H. meleagridis. Shotgun proteomics, aided by customized database, identified 176 proteins including actin, potential moonlighting glycolytic enzymes, lytic molecules such as pore-forming proteins (PFPs) and proteases like cathepsin-L like cysteine protease. To quantify the exoproteomic differences between the virulent and the attenuated H. meleagridis cultures, a sequential window acquisition of all theoretical spectra mass spectrometric (SWATH-MS) approach was applied. Surprisingly results showed most of the exoproteomic differences to be of bacterial origin, involving metabolism and locomotion. By deciphering such molecular signatures, novel insights into an inherent complex in vitro protozoan- bacteria relationship was elucidated.

2019-02-11 | PXD012037 | Pride

Post-covid surgical complications in adipose tissue

Project description:Spinal cord injury (SCI) patients who underwent reconstructive surgery for pressure ulcers (PU) within 4 weeks of positive SARS-CoV-2 diagnosis were included in this study. Patient’s post-operative progression was registered, while the adipose tissue surrounding the ulcers was analyzed by proteomic and immunohistochemical assays to identify molecular/cellular signatures of impaired recovery.

2022-05-20 | PXD031241 | Pride

Shotgun proteomic profiling of intestinal mucosa of rainbow trout Oncorhynchus mykiss

Project description:The objective of this study was to identify and quantify proteomic profiles of intestine of rainbow trout (Oncorhynchus mykiss). Specific pathogen free rainbow trout (mean length 15 ± 1 cm) were maintained in recirculating de-chlorinated water at 19±1 °C. Prior to the experiment, fish were distributed between aquaria. The test groups were infected by immersion of Yersinia ruckeri CSF007-82 (biotype 1) and 7959-11 (biotype 2) strains. The control group was immersed similar with sterile broth medium. Fish were anaesthetized and sampled aseptically at different time points. Each intestine was washed three times with sterile phosphate-buffered saline containing a cocktail of mammalian protease inhibitors. Intestinal mucosa was scraped with a sterile large scalpel blade. Intestinal samples were snap-frozen in liquid nitrogen and stored at –80 °C.

2019-11-12 | PXD011087 | Pride

Gas5 RIP-LC MS/MS using PFC lysates from behavioral-trained mice

Project description:Long noncoding RNAs (lncRNAs) represent a multidimensional class of regulatory molecules that are involved in many aspects of brain function. Emerging evidence indicates that lncRNAs are localized to the synapse; however, a direct role for their activity in this subcellular compartment in memory formation has yet to be demonstrated. Using lncRNA capture-seq, we identified a Gas5 variant that accumulate in the synaptic compartment within the infralimbic prefrontal cortex of adult male C57/Bl6 mice. Gas5 RNA immunoprecipitation followed by mass spectrometry revealed that this Gas5 isoform, in association with the RNA binding proteins G3BP2 and CAPRIN1, regulates the activity-dependent trafficking and clustering of RNA granules. In addition, we found that cell-type-specific, activity-dependent, and synapse-specific knockdown of this Gas5 variant led to impaired fear extinction memory. These findings identify a new mechanism of fear extinction that involves the dynamic interaction between local lncRNA activity and RNA condensates in the synaptic compartment.

2023-11-20 | PXD046479 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data