Project description:HEK293T cells were labeled with either AHA or hAHA without any treatment. This datasets refers to one biological replicate from null experiments using HILAQ so people can use it as a test dataset. That dataset will provide quantitative information of ~3,000 proteins and ~25,000 peptides.
Project description:Development of an improved workflow for newly synthesized proteome analysis, based on combined pulsed metabolic labelling with L-azidohomoalanine (AHA) and semi-automated click chemistry-based enrichments with magnetic alkyne agarose beads.
Project description:Bioorthogonal chemistry introduces affinity-labels into biomolecules with minimal disruption to the original system and is widely applicable in a range of contexts. In proteomics, immobilized metal affinity chromatography (IMAC) enables enrichment of phosphopeptides with extreme sensitivity and selectivity. Here, we adapt and combine these superb assets in a new enrichment strategy using phosphonate-handles, which we term ‘PhosID’. In this approach, ‘click-able’ phosphonate-handles are introduced into proteins via 1,3-dipolar Huisgen-cycloaddition to azido-homo-alanine (AHA) and IMAC is then used to enrich exclusively for phosphonate-labeled peptides. In interferon-gamma (IFNγ) stimulated cells, PhosID enabled the identification of a large number of IFN responsive newly synthesized proteins (NSPs) whereby we monitored the differential synthesis of these proteins over time. Collectively, these data validate the excellent performance of PhosID with efficient analysis and quantification of hundreds of NSPs by single LC-MS/MS runs. We envision PhosID as an attractive and alternative tool for studying stimuli-sensitive proteome subsets.
Project description:Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) followed by high-throughput sequencing of RBM7-associated transcripts. Note: these data relate to Figure 1, 2, 3, 4, 5 and 6 in Lubas, Andersen et al., Cell Reports 2014
Project description:Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) followed by high-throughput sequencing of RBM7-associated transcripts. Note: these data relate to Figure 1, 2, 3, 4, 5 and 6 in Lubas, Andersen et al., Cell Reports 2014 RBM7-associated transcripts
Project description:The recently introduced cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) technique enables protein-RNA cross-links to be used as precisely localized distance restraints in de novo structural modelling, but little is known about the structural characteristics of UV-induced cross-links. Here we demonstrate protocol optimizations, and apply the enhanced protocol to a set of model protein-RNA complexes to better characterize the properties of UV-induced protein-RNA cross-links. We use these insights to study a non-canonical protein-RNA interaction between SF3A1 of the U2 snRNP and stem-loop 4 of the U1 snRNP, demonstrating that UV cross-linking and mass spectrometry is a reliable standalone data type for low resolution structural characterizations of protein-RNA interactions.
Project description:Cell tracking is enabled by incubating ex vivo cells with commercially/clinically available MRI particulate label, such as ferucarbotran. However, the uptake by non-phagocytic cells, such as mesenchymal stem cell (MSC) is poor, and the detection by MRI is impeded. MGIO is a new label that is efficiently taken up by MSC. The proliferation and differentiation capacity of labelled cells are usually assessed to determine cytotoxicity. In this study, we compared the global gene expression profiles of mock-labelled, ferucarbotran-labelled and MGIO-labelled fetal MSC.
Project description:SILAC labelled peptides from control and UV or 2-deoxy glucose treated A549 cells. Control is light labelled and treatment groups are heavy labelled. Fractions are as per below:
UV1: APM-0331-2 to APM-0331-6
UV2: APM-0331-12 to APM-0331-16
2DG1: APM-0331-7 to APM-0331-11
2DG2: APM-0331-17 to APM-0331-21
Project description:The determination of thiabendazole is crucial for ensuring food safety, environmental protection, and compliance with regulatory standards. Accurate detection helps prevent harmful exposure, ensuring the safety of agricultural products and safeguarding public health. Therefore, this study investigates the electrochemical sensing capabilities of newly synthesized oligo 3-amino-5-mercapto-1,2,4-triazole (oligo AMTa) using hydrogen tetrachloroaurate (III) (HAuCl4) as an oxidizing agent at room temperature for thiabendazole (TBZ) detection, employing a simple electrode fabrication process. The prepared oligo AMTa was thoroughly characterized using UV-visible spectroscopy, scanning electron microscopy (SEM), Energy Dispersive X-ray Analysis (EDAX), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), high-resolution mass spectroscopy (HR-MS), and Fourier-transform infrared spectroscopy (FT-IR) to confirm its oligomerization structure and properties. The IR spectrum of oligo AMTa reveals a new peak at 1449 cm-1, indicating the conversion of -NH2 groups to -N=N- groups during oligomerization, unlike AMTa. Additionally, the disappearance of the -SH group peak at 2615 cm-1 in oligo AMTa suggests an S-S linkage involvement in the oligomerization process. In the oligo AMTa XPS spectrum, the presence of C=N is displayed by a small peak at 287.3 eV, and oligomerization via -NH and N=N is confirmed by the lack of a 284.0 eV peak for C-C or C=C. Gold nanoparticle formation is not demonstrated by the 84.8 eV peak, which implies that the gold atom is not in the Au0 state. The HR-MS spectrum of oligo AMTa shows a peak at m/z 564.08, indicating a chain of five monomers, and another peak at m/z 435.03, confirming the presence of a tetrameric form of AMTa. After that, the GC electrode was directly linked to the oligo AMTa by the potentiodynamic method. SEM, electrochemical impedance spectroscopy (EIS), and cyclic voltammetry (CV) were all employed to confirm the fabrication of oligo AMTa. The SEM image illustrates the formation of a particlelike structure with a uniform size of the oligomer after cycling in 0.1 M H2SO4. After electrocycling, the size of the oligomer was reduced from 2.6 μm to 30 nm. The oligo AMTa-modified electrode possesses the highest electroactive surface area and electrical conductivity due to several key factors. First, the presence of amino (-NH2) and thiol (-SH) functional groups in AMTa enhances the surface coverage and density of electroactive sites, increasing the electroactive surface area. Additionally, the conjugated structure of AMTa facilitates efficient electron transfer, resulting in enhanced electrical conductivity compared to unmodified electrodes. Eventually, the electrochemical oxidation of TBZ occurred using the fabricated electrodes. The GC/oligo AMTa electrode exhibited a four-fold increase in oxidation current for TBZ compared to unmodified GC electrodes. This enhancement is due to the improved surface properties from the oligo AMTa modification, which significantly boosts TBZ adsorption through strong interactions like hydrogen bonding and π-π stacking. These interactions, along with the increased surface area and catalytic properties, facilitate effective electron transfer, resulting in a higher oxidation current. As an outcome, the film was employed to determine the sensitivity level of TBZ, and a LOD of 1.8 × 10-11 M (S/N = 3) was found. The straightforward method's practical utility was proven by measuring TBZ in tap water, water spinach, and pear juice samples. The comprehensive characterization of oligo AMTa provided insights into its interaction mechanisms with thiabendazole, contributing to the development of a reliable, cost-effective, and efficient sensor.
Project description:The ongoing search for effective treatment of Acne vulgaris is concentrated, i.a., on natural peptides with antimicrobial properties. The aim of this work was the development of new amino acid derivatives with potential activity on dermal infections against selected microorganisms, including the facultative anaerobe C. acne. The peptides P1-P6 were synthesized via Fmoc solid phase peptide synthesis using Rink amide AM resin, analyzed by RP-HPLC-MS, FTIR, DPPH radical scavenging activity, and evaluated against C. acne and S. aureus, both deposited and non-deposited in BC. Peptides P1-P6 presented a lack of cytotoxicity, antimicrobial activity, or antioxidative properties correlated with selected structural properties. P2 and P4-P6 sorption in BC resulted in variable data, i.a., confirming the prospective topical application of these peptides in a BC carrier.