Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Penicillium expansum Blistering1

ABSTRACT: TMT 6-plex of P. expansum R19 and T625 mycelia. 14 files represent 12 concatenated fractions and 2 void volumes from reverse phase high pH HPLC separation of pooled TMT samples (prefix WJ2). Media proteins from P. expansum R19 and T625. 3 files (prefix BC018) are reps for wildtype R19 control. 3 files (prefix T6) are reps for transformant T625

INSTRUMENT(S): Lumos

ORGANISM(S): Penicillium Expansum (ncbitaxon:27334)

SUBMITTER: Bret Cooper

PROVIDER: MSV000082957 | MassIVE |

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Similar Datasets

Evaluation of differential peptide loading on TMT-based proteomic and phosphoproteomic data quality

Project description:Investigating the impacts on MS data quantitation reproducibility when loading differential amounts of peptides, ranging from 20 to 400 ug, across channels of TMT 11 multiplexes. PTRC_Exp9 files represent global proteome and phosphoproteome data generated from PBMCs isolated from AML patients, acquired through 12 fractions and 6 fractions per plex, respectively. In this experiment, TMT channels were loaded with varying peptide quantities ranging from 20 to 400 ug. PTRC_Exp12 files represent proteomic and phosphoproteomic data from the MOLM-14 AML cell line, also acquired across 12 global proteomics fractions and 6 phosphoproteomics fractions per plex. In this experiment, all TMT channels were loaded with equivalent quantity of peptides (400 ug). Samples were reduced with dithiothreitol, alkylated with iodoacetamide, and double-digested with Lys-C and trypsin. Digested peptides were desalted with C18 SPE columns, labeled with TMT11 isobaric tags, and fractionated by high pH reverse phase separation. After aliquots were removed for global proteomics (12 fractions per plex), samples were concatenated and IMAC was used to enrich phosphopeptides (6 fractions per plex). LC-MS/MS measurements were acquired on an Orbitrap Fusion Lumos mass spectrometer.

2020-11-05 | MSV000086417 | MassIVE

Proteomic profiling of RNase III-dependent asRNA regulation in E. coli

Project description:In an effort to determine if the RNase III-dependent asRNA regulation had an effect on protein production in E. coli we conducted two TMT 6-plex experiments comparing cultures of wildtype E. coli, rnc-14, rnc-38, hfq in the stationary and exponential phase.

2020-06-18 | PXD011180 | Pride

Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4 (ChIP-seq)

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

Concatenated small PCRs

Project description:Concatenated small PCRs

| PRJEB2224 | ENA

Expression Analysis of Trimethyltin Chlorides (TMT) Impact on Embryonic Development

Project description:Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control Embryos were exposed to 10uM TMT or control from 48hpf to 60 or 72 hpf. Three replicates were collected for each time point. 40 embryos were pooled to comprise a replicate.

2011-03-23 | E-GEOD-28131 | biostudies-arrayexpress

Microarray analysis of the effects of a Î³-tocopherol-rich mixture of tocopherols on global gene expression in the prostates of TRAMP mice

Project description:We used whole mouse genome microarrays to the effects of Î³-TmT on global gene expression in the prostate TRAMP and age-matched C57BL/6 mice were administered either 600 mg/kg of Î³-TmT or a control vehicle via oral gavage. Twelve hours after dosing, prostate tissues were collected for RNA extraction.

2014-09-16 | E-GEOD-61416 | biostudies-arrayexpress

Control vs Elp3-deficient mouse myeloid progenitors 6-plex TMT LC-MSMS

Project description:6-plex TMT LC-MSMS quantification of proteins in myeloid progenitors (Lineage- Sca1- Kit+ cells) isolated from the bone marrow of 8-12 week old male and female control and Elp3-deficient (Elp3fl/fl vav-iCreT/+) mice. Biological triplicates of each genotype were analyzed, each consisting of 1.10e6 cells from pools of 12-14 control (Elp3fl/fl) or 26-38 (Elp3-deficient) male and female mice.

2021-01-26 | PXD010486 | Pride

Omics Reveal Far Reaching Effects of Verapamil Treatment in Subjects with Type 1 Diabetes

Project description:Proteomic data from recent onset T1D patients treated with verapamil where significant extension of the honeymoon phase was observed. Samples were depleted with MARS Hu-14 column, digested with trypsin, labeled with 11-plex TMT, then analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline. TMT data was extracted using PlexedPiper.

2021-06-09 | MSV000087598 | MassIVE

Concentrations of 27 cytokines and chemokines in the culture medium of HUVECs

Project description:Culture medium of HUVECs was collected and analyzed with the Bio-Plex Pro™ Human Cytokine 27-plex Panel.

2023-11-07 | GSE246852 | GEO

27-plex Tandem Mass Tag Mass Spectrometry for Profiling Brain Proteome in Alzheimer's Disease

Project description:Systematically optimized the protocol for the newly developed 16-plex TMT Reported a novel 27-plex method to enhance the multiplexity for large-scale proteomic profiling, by combining two sets of distinct isobaric tags (11-plex and 16-plex TMT) based on their disparate mass shifts on modified peptides.

2021-04-09 | PXD025261 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data