Similar Datasets
Project description:Updated VC N16961 reference genome
| PRJEB22249 | ENA
Project description:The in-gel digestion of proteins for analysis by liquid chromatograph mass spectrometry has been used since the early 1990s. Although several improvements have contributed to increasing the quality of the data obtained, many recent publications still use sub-optimal approaches. We present an updated in-gel digestion protocol. We show that alternative reducing, alkylating agents and tryptic digestion buffers increase peptide and protein identification and reduce incubation times. Our results indicate that a simultaneous and short, high temperature reduction and alkylation reaction using Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) and chloroacetamide (CAA) with a subsequent gel wash improve protein identification and sequence coverage, diminish peptide side reactions. Additionally, use of 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid buffer (HEPES) allows a significant reduction in the digestion time improving trypsin performance and increasing the peptide recovery. The updated in-gel digestion protocol described here is highly efficient and offers flexibility to be incorporated in any proteomic laboratory.
2018-10-02 | PXD009600 | Pride
Project description:Development of an updated genome-scale metabolic model of Clostridium thermocellum and its application for integration of multi-omics datasets
2019-10-22 | MSV000084488 | MassIVE
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-12-31 | GSE148211 | GEO
Project description:<TO BE UPDATED> Chronic lymphocytic leukaemia (CLL) is a common, adult B-cell leukaemia that has challenges in prognosis and treatment. It is characterised by a heterogeneous clinical course with multiple distinct phenotypes currently defined genetically or with target-specific monoclonal antibodies. While many studies have examined specific protein targets or global mRNA expression in CLL, few have attempted to characterise expression across the whole proteome. To achieve a non-biased, global proteomics characterisation, 14 CLL samples representing the genetic mutant subgroups NOTCH1, SF3B1 and WT, were subjected to quantitative mass spectrometry and compared with normal B cells using two isobaric tag experiments (TMT 10-plex). 6150 proteins were fully quantitated revealing a strong correlation between the regulated proteins across the CLL samples, independent of subtype. >800 proteins demonstrated significant upregulation (p<0.05) across the CLL samples. In addition to several novel cell surface markers, overexpressed proteins were strongly indicative of dysregulation to mRNA processing, spliceosome activity, transcriptional control by RNA pol II and epigenetic mechanisms (all p<10-10). A strong enrichment was observed for proteins coded by chromosome 12, often observed with trisomy in CLL (p<0.001). Downregulated proteins included cell adhesion molecules such as integrins and suggested a reduced capacity for endothelial transmigration (both p<10-10). These findings confirm many previous observations of CLL-specific protein overexpression (eg. CD5, ROR1, matriptase) and identify several novel surface targets for investigation. They also suggest that strong patterns of protein expression exist across CLL subtypes. Together, these results demonstrate the potential of proteomics and advocate the characterisation of further cancer samples by such methods.
2018-01-26 | PXD002004 | Pride
Project description:We conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility.
2023-07-04 | GSE228820 | GEO
Project description:This is a new version of a liver iron model (original from Mitchell 2013 BIOMD0000000498) with updated kinetics of ferritin iron storage. It uses MODEL2211030001 as a substitute for the original ferritin reactions.
2023-02-07 | MODEL2211030002 | BioModels
Project description:Plasma samples from HNRC for low biomass protocol testing. Data was acquired using a Bruker Maxis Impact and C18 RP-UHPLC. Positive polarity acquisition of LC-MS/MS. Updated files here.
2020-07-11 | MSV000085724 | GNPS
Project description:<p>MAVEN, an open-source software program for analysis of LC-MS metabolomics data, was originally released in 2010. As mass spectrometry has advanced in the intervening years, MAVEN has been periodically updated to reflect this advancement. This manuscript describes a major update to the program, MAVEN2, which supports LC-MS/MS analysis of metabolomics and lipidomics samples. We have developed algorithms to support MS/MS spectral matching and efficient search of large-scale fragmentation libraries. We explore the ability of our approach to separate authentic from spurious metabolite identifications using a set of standards spiked into water and yeast backgrounds. To support our improved lipid identification workflow, we introduce a novel <em>in-silico</em> lipidomics library covering major lipid classes and compare searches using our novel library to searches with existing <em>in-silico</em> lipidomics libraries. MAVEN2 source code and cross-platform application installers are freely available for download from GitHub under a GNU permissive license [ver 3], as are the in silico lipidomics libraries and corresponding code repository.</p>
2024-07-22 | MTBLS3097 | MetaboLights