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