GNPS-compositae_MN library_240115
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Exploris 120
ORGANISM(S): Asteraceae (ncbitaxon:4210)
SUBMITTER: 
Heejung Yang
PROVIDER: MSV000093868 | GNPS | Sun Jan 14 21:36:00 GMT 2024
REPOSITORIES: GNPS
Similar Datasets
Project description:This dataset consists of in silico generated TOF top-down proteomics spectra created using the FTMS simulator software (Spectroswiss). The simulated datasets are designed to evaluate FDR estimation in spectral deconvolution. Protein sequences were used to generate MS datasets with varying resolution, noise, and charge characteristics. The dataset includes deconvolved TSV files and corresponding input mzML insilico file.
2026-03-09 | PXD063631 | Pride
Project description:We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. To benchmark this method, we measured twenty pure culture species using the Direct Protein-SIF method as well as Isotope Ratio Mass Spectrometry. Some of the pure cultures were measured in technical replicates to see how consistent Protein-SIF measurements are between mass spec runs. This submission thus contains 29 raw files for the pure cultures. See table in the submission for details of which species was measured for which .raw file. We also included the Direct Protein-SIF specific isotope pattern files as well as the .mzML files and PSM files required as input for the Direct Protein-SIF software. In addition to the pure culture a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are also included in this submission (see publication for details on how the reference material is used to calibrate the method).
2018-05-21 | PXD006762 | Pride
Project description:Observational, Multicenter, Post-market, Minimal risk, Prospective data collection of PillCam SB3 videos (including PillCam reports) and raw data files and optional collection of Eneteroscopy reports
| 2291850 | ecrin-mdr-crc
Project description:This dataset consists of in silico generated Orbitrap top-down proteomics spectra created using the FTMS simulator software (Spectroswiss). The simulated datasets are designed to evaluate false discovery rate (FDR) estimation in spectral deconvolution workflows. Protein sequences were used to generate MS spectra with varying resolution, noise, and charge characteristics. The dataset includes deconvolved TSV files and corresponding mzML spectra for each simulated run.
2026-03-09 | PXD063573 | Pride
Project description:Temporal analysis of Irf4 and PU.1 genome binding during B cell activation and differentiation in vitro using antigen (NP-Ficoll) CD40L and IL-2/4/5 cytokines (see Molecular Systems Biology 7:495 for details of cellular system). The results provide insight in the target genes and binding specificity of IRF4 and PU.1 during coordination of different programs of B cell differentiation. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format.
2013-05-04 | GSE46607 | GEO
Project description:<p>Despite untargeted LC-MS/MS data being a powerful approach for large-scale metabolomics analysis, a significant challenge in the field lies in the reproducible and efficient analysis of such data, in particular. The power of R-based analysis workflows lies in their high customizability and adaptability to specific instrumental and experimental setups, but, while various specialized packages exist for individual analysis steps, their seamless integration and application to large cohort datasets remains elusive. Addressing this gap, we present an comprehensible end-to-end R workflow that leverages <em>xcms</em> and packages of the <em>RforMassSpectrometry</em> environment to encompass all aspects of pre-processing and downstream analyses for LC-MS/MS datasets in a reproducible manner.</p><p>This workflow delineates a step-by-step analysis of an example untargeted metabolomics dataset tailored to quantify the small polar metabolome in human plasma samples and aimed to identify differences between individuals suffering from a cardiovascular disease and healthy controls. The objective of the workflow is to meticulously detail each step, from the preprocessing of raw mzML files to the annotation of differentially abundant ions between the two groups. Our workflow seamlessly integrates Bioconductor packages, offering adaptability to diverse study designs and analysis requirements.</p><p>This workflow facilitates preprocessing, feature detection, alignment, normalization, statistical analysis and annotation within a unified framework, thereby enhancing the efficiency of metabolomic investigations. We also discuss alternative approaches to accommodate various dataset and goals, while emphasizing proper quality management for LC-MS data analysis. The source code of the workflow is available at https://github.com/EuracBiomedicalResearch/end-to-end-untargeted-metabolomics.</p>
2024-08-26 | MTBLS8735 | MetaboLights
Project description:The locations of mammalian recombination hotspots are determined by PRDM9, a zinc finger histone methyltransferase that locally trimethylates histone H3 at residues K4 and K36. We previously reported two hypomorphic catalytic mutations, Prdm9-EP and Prdm9-EK, with different phenotypic effects. Prdm9-EP, but not Prdm9-EK, is compatible with female sub-fertility, while both mutations phenocopy the Prdm9-null condition in males. Here we directly compare and contrast the enzymatic effects of the two mutations in vitro and in vivo. We previously performed two biological H3K4me3 ChIP-seq replicates in spermatocytes isolated from Prdm9-EP homozygous males (GSE144144; SRX8588740 and SRX8588741), and re-processed previously reported H3K4me3 ChIP-seq data from spermatocytes isolated from wild-type B6 males (GSE52628; SRX381465 and SRX381466). We used those raw and processed files for this study (GSE144144). We also previously performed one biological H3K4me3 replicate in spermatocytes isolated from Prdm9-EP homozygous males (GSE112110; SRX4136625). We report an additional replicate here, and merged the two replicates for analysis; raw and processed files are reported here. We also performed ChIP-seq for H3K36me3 in both Prdm9-EP and Prdm9-EK homozygous spermatocytes. Raw and processed files are available here. For comparison, we re-mapped and re-analyzed H3K36me3 ChIP-seq data we previously reported from wild-type B6 spermatocytes (GSE76416; SRX1508234); processed files are available here.
2021-10-11 | GSE181479 | GEO
Project description:The transcription factor IRF4 regulates immunoglobulin class switch recombination and plasma cell differentiation. Its differing concentrations appear to regulate mutually antagonistic programs of B and plasma cell gene expression. We show IRF4 to be also required for generation of germinal center (GC) B cells. Its transient expression in vivo induced the expression of key GC genes including Bcl6 and Aicda. In contrast, sustained and higher concentrations of IRF4 promoted the generation of plasma cells while antagonizing the GC fate. IRF4 cobound with the transcription factors PU.1 or BATF to Ets or AP-1 composite motifs, associated with genes involved in B cell activation and the GC response. At higher concentrations, IRF4 binding shifted to interferon sequence response motifs; these enriched for genes involved in plasma cell differentiation. Our results support a model of "kinetic control" in which signaling-induced dynamics of IRF4 in activated B cells control their cell-fate outcomes. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format.
2013-05-04 | GSE46608 | GEO
Project description:We have used HiRIEF (High Resolution Isoelectric Focusing) LC-MS proteomics (Branca et al., 2014, PMID: 24240322) with isobaric tags (TMT10plex) to compare 32 post-mortem human brains in the prefrontal cortex (Brodmann areas 24 and 40) of prospectively followed patients with Alzheimer`s disease (AD), Parkinson`s disease with dementia (PDD), dementia with Lewy bodies (DLB) and older adults without dementia. LCMS raw files deposited here refer to samples from BA24 and BA40. For BA09 raw files, refer to the older dataset PXD006122. Proteomics database search files for all three Brodmann areas (BA09, BA24 and BA40) are posted here.
2024-06-10 | PXD047324 | Pride
Project description:Raw fastq files from paired-end, Illumina-based sequencing on NovaSeq6000
2021-11-01 | GSE160615 | GEO