Search results for "PROTEOMICS"
showing 10 items of 534 documents
Proteome adaptations under contrasting soil phosphate regimes of Rhizophagus irregularis engaged in a common mycorrhizal network.
2021
International audience; For many plants, their symbiosis with arbuscular mycorrhizal fungi plays a key role in the acquisition of mineral nutrients such as inorganic phosphate (Pi), in exchange for assimilated carbon. To study gene regulation and function in the symbiotic partners, we and others have used compartmented microcosms in which the extra-radical mycelium (ERM), responsible for mineral nutrient supply for the plants, was separated by fine nylon nets from the associated host roots and could be harvested and analysed in isolation. Here, we used such a model system to perform a quantitative comparative protein profiling of the ERM of Rhizophagus irregularis BEG75, forming a common my…
Neuroproteomics in the auditory brainstem: candidate proteins for ultrafast and precise information processing.
2014
In the mammalian auditory brainstem, the cochlear nuclear complex (CN) and the superior olivary complex (SOC) feature structural and functional specializations for ultrafast (<1 ms) and precise information processing. Their proteome, the basis for structure and function, has been rarely analyzed so far. Here we identified and quantified the protein profiles of three major auditory brainstem regions of adult rats, the CN, the SOC, and the inferior colliculus (IC). The rest of the brain served as a reference. Via label-free quantitative mass spectrometry and 2-D DIGE/MALDI-MS, we identified 584 and 297 proteins in the plasma membrane/synaptic vesicle proteome and the cytosolic proteome, respe…
Mass spectrometry applications
2012
The history of proteomics dates back to the discovery of two-dimensional gels in the 1970s, which provided the first feasible way of displaying hundreds or thousands of proteins on a single gel. Despite mass spectrometry being restricted for a long time to small and thermostable compounds, the development in the late 1980s of two techniques for the routine and general formation of molecular ions of intact biomolecules changed this situation and mass spectrometry has become an indispensable tool for proteomics research. The aim of this chapter is to review the major types of MS instruments used in proteomics analysis and to discuss strategies for the analysis of whole proteins and peptides o…
Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics.
2013
A data-independent acquisition (DIA) mass spectrometry approach, ultradefinition (UD)MSE, offers high reproducibility and improved proteome coverage over alternative DIA and data-dependent acquisition workflows. We present a data-independent acquisition mass spectrometry method, ultradefinition (UD) MSE. This approach utilizes ion mobility drift time-specific collision-energy profiles to enhance precursor fragmentation efficiency over current MSE and high-definition (HD) MSE data-independent acquisition techniques. UDMSE provided high reproducibility and substantially improved proteome coverage of the HeLa cell proteome compared to previous implementations of MSE, and it also outperformed a…
Proteomic Analyses Reveal an Acidic Prime Side Specificity for the Astacin Metalloprotease Family Reflected by Physiological Substrates
2011
Astacins are secreted and membrane-bound metalloproteases with clear associations to many important pathological and physiological processes. Yet with only a few substrates described their biological roles are enigmatic. Moreover, the lack of knowledge of astacin cleavage site specificities hampers assay and drug development. Using PICS (proteomic identification of protease cleavage site specificity) and TAILS (terminal amine isotopic labeling of substrates) degradomics approaches >3000 cleavage sites were proteomically identified for five different astacins. Such broad coverage enables family-wide determination of specificities N- and C-terminal to the scissile peptide bond. Remarkably, me…
Exosomes released by keratinocytes modulate melanocyte pigmentation
2015
Cells secrete extracellular vesicles (EVs), exosomes and microvesicles, which transfer proteins, lipids and RNAs to regulate recipient cell functions. Skin pigmentation relies on a tight dialogue between keratinocytes and melanocytes in the epidermis. Here we report that exosomes secreted by keratinocytes enhance melanin synthesis by increasing both the expression and activity of melanosomal proteins. Furthermore, we show that the function of keratinocyte-derived exosomes is phototype-dependent and is modulated by ultraviolet B. In sum, this study uncovers an important physiological function for exosomes in human pigmentation and opens new avenues in our understanding of how pigmentation is…
Quantitative Proteome and Phosphoproteome Profiling in Magnaporthe oryzae
2021
The quality and consistency in every sample preparation procedure is crucial for any scientific output. Therefore, it is of utmost importance to have easy, economic, and robust sample preparation protocols. Here, we describe a simple and robust bottom-up proteomic sample preparation strategy for identification and label-free quantification (LFQ) of proteins and phosphoproteins. The presented workflow is designed for large-scale application and involves easy scalable and well-known robust sample preparation techniques, such as cell lysis with SDS buffer under heat, protein precipitation using methanol/chloroform, tryptic digest, and commercially available TiO2 phosphopeptide enrichment kits.…
Lipopolysaccharide‐regulated secretion of soluble and vesicle‐based proteins from a panel of colorectal cancer cell lines
2021
Purpose To mimic the perioperative microenvironment where bacterial products get in contact with colorectal cancer (CRC) cells and study its impact on protein release, we exposed six CRC cell lines to lipopolysaccharide (LPS) and investigated the effect on the secretome using in-depth mass spectrometry-based proteomics. Experimental design Cancer cell secretome was harvested in bio-duplicate after LPS treatment, and separated in EV and soluble secretome (SS) fractions. Gel-fractionated proteins were analysed by label-free nano-liquid chromatography coupled to tandem mass spectrometry. NF-κB activation, triggered upon LPS treatment, was evaluated. Results We report a CRC secretome dataset of…
Brain protein expression changes in WAG/Rij rats, a genetic rat model of absence epilepsy after peripheral lipopolysaccharide treatment
2013
Peripheral injection of bacterial lipopolysaccharide (LPS) facilitates 8–10 Hz spike-wave discharges (SWD) characterizing absence epilepsy in WAG/Rij rats. It is unknown however, whether peripherally administered LPS is able to alter the generator areas of epileptic activity at the molecular level. We injected 1 mg/kg dose of LPS intraperitoneally into WAG/Rij rats, recorded the body temperature and EEG, and examined the protein expression changes of the proteome 12 h after injection in the fronto-parietal cortex and thalamus. We used fluorescent two-dimensional differential gel electrophoresis to investigate the expression profile. We found 16 differentially expressed proteins in the front…
Redox Proteomics of the Inflammatory Secretome Identifies a Common Set of Redoxins and Other Glutathionylated Proteins Released in Inflammation, Infl…
2015
Protein cysteines can form transient disulfides with glutathione (GSH), resulting in the production of glutathionylated proteins, and this process is regarded as a mechanism by which the redox state of the cell can regulate protein function. Most studies on redox regulation of immunity have focused on intracellular proteins. In this study we have used redox proteomics to identify those proteins released in glutathionylated form by macrophages stimulated with lipopolysaccharide (LPS) after pre-loading the cells with biotinylated GSH. Of the several proteins identified in the redox secretome, we have selected a number for validation. Proteomic analysis indicated that LPS stimulated the releas…