Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic and lipidomic analysis of Ground Demonstrator Model of ArtEMISS-C, MELiSSA Project on Limnospira indica PCC 8005 P3.

ABSTRACT: Proteomic and lipidomic analysis of Ground Demonstrator Model of ArtEMISS-C (Science Verification Test), MELiSSA Project on Limnospira indica PCC 8005 P3. Proteomic analysis has been performed with AB Sciex TripleTOF 6600. Lipidomic analysis has been performed with AB Sciex ZenoTOF 7600.

INSTRUMENT(S): TripleTOF 6600, ZenoTOF 7600

ORGANISM(S): Limnospira Indica (ncbitaxon:147322)

SUBMITTER: Cecile Renaud

PROVIDER: MSV000094881 | MassIVE | Tue May 28 06:57:00 BST 2024

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

High-throughput proteomics and phosphoproteomics of rat tissues using micro-flow Zeno SWATH

Project description:We investigated the combined sensitivity of micro-flow liquid chromatography with a ZenoTOF mass spectrometer for high throughput proteomic and phosphoproteomic analysis of rat tissues. Comparing the proteomes acquired using data-independent acquisition (DIA) on the ZenoTOF 7600 with the previous generation TripleTOF 6600, more proteins were quantified using a fifth of the sample load and a third of the instrument time. Zeno SWATH data was evaluated using replicate injections of rat organ digests to compare FragPipe and DIA-NN computational pipelines. FragPipe identified more proteins in 7 of the 8 rat organs, with an extra 12% and 17% observed in heart and muscle tissue respectively. The number of identified peptides per protein were higher with FragPipe and the precision of missing values across replicate injections was more consistent. Single-shot phosphopeptide enrichment from 100 µg rat tissue, without fractionation, was acquired using data-dependent acquisition (DDA) on both instruments. A total of 5,108 phosphosites were quantified with a negligible increase in phosphosites found using the ZenoTOF 7600 relative to the 6600. Using DIA on the ZenoTOF, 8,013 phosphosites were quantified using Spectronaut.

2024-06-02 | PXD045472 | Pride

Electron-Activated Dissociation and Collision-Induced Dissociation Glycopeptide Fragmentation for Improved Glycoproteomics

Project description:Protein glycosylation is a critical PTM for the stability and biological function of many proteins, but full characterisation of site-specific glycosylation of proteins remains analytically challenging. Collision induced dissociation (CID) is the most common fragmentation method used in LC-MS/MS workflows, but loss of labile modifications render CID inappropriate for detailed characterisation of site-specific glycosylation. Electron-based dissociation (ExD) methods provide alternatives that retain intact glycopeptide fragments for unambiguous site localisation, but these methods often underperform CID due to increased reaction times and reduced efficiency. Electron activated dissociation (EAD) is another strategy for glycopeptide fragmentation. Here, we use a ZenoTOF 7600 SCIEX instrument to compare the performance of various fragmentation techniques for the analysis of a complex mixture of mammalian O- and N-glycopeptides.

2024-07-04 | PXD050173 | Pride

Metabolomics analysis of mouse gut microbiota

Project description:Liquid chromatography -mass spectrometry was performed on an AB Sciex TripleTOF 5600TM mass spectrometry system (AB SCIEX, USA) for nontargeted metabolomics analysis

2022-04-24 | PXD033405 |

The dataset to discover ESCC related proteins

Project description:To discover ESCC related proteins, we used SWATH to quantify the protein abundance between ESCC and adjacent tissues. Briefly, we pooled 10 ESCCtissues and their corresponding adjacent tissues for SWATH acquisition with three replicates.Three DDA repeats were also acquired with the pooled 10-paired ESCC tissue.The trypsin digested peptide mixture was analyzed by AB SCIEX 5600 (AB SCIEX).The database searching procedure was achieved using ProteinPilot v4.5 (AB Sciex). The database is IPI_homo_sapiens_V3.87.

2015-09-22 | PXD001764 | Pride

Transcriptomic and lipidomic analyses unravel the responses of Faecalibacterium prausnitzii to calcium palmitate

Project description:We investigate the underlying mechanism of the CP inhibition on F. prausnitzii by analysing its effects at the transcriptomic and lipidomic levels.

2024-03-01 | GSE225701 | GEO

Triple acquisition mass spectrometry (TRAM) combining targeted and non-targeted metabolomics in a single run

Project description:Data was acquired in TRAM (DDA+MRM), DDA-only, and MRM-only mode on a ZenoTOF 7600 with alkaline HILIC separation.

2024-05-08 | MSV000094712 | MassIVE

Cytosol - Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism

Project description:Enriched Arabidopsis cytosol (cell culture) fractionated by SCX (15 fractions) and analysed by Q-TOF nanoLC-MS/MS (AB Sciex QStar Elite)

2011-03-01 | PRD000391 | Pride

SWATH-MS dataset of Garcinia mangostana pericarp’s proteome across ripening stages

Project description:Data provided is derived from our research on comparing protein expression profiling of Garcinia mangostana (G. mangostana) Linn. on different ripening stages. Proteins were extracted from the pericarp of G. mangostana at three points of ripening stages (stage 0, 2 and 6) and digested with trypsin before being analyzed using 1 Dimensional and 2 Dimensional Information Dependent Acquisition Liquid Chromatography (1D and 2D IDA LC) coupled with sequential window acquisition of all theoretical fragment ion spectra (SWATH) analysis. This approach enable us to identify and relatively quantify protein in complex mixture. Protein identification was performed by matching tandem mass (MS/MS) spectra from 1D and 2D IDA to in-house-generated and UniProt databases using a database search algorithm software ProteinPilot (v4.2) (AB Sciex). Protein quantification was performed by analyzing protein peak areas extracted from SWATH analysis data sets using PeakView (v2.1) (AB Sciex) software. Finally, protein peaks were subjected to statistical analysis to compare relative protein peak areas between the sample groups.

2021-05-24 | PXD006295 | Pride

Evaluation of the carrier proteome limit on a ZenoTOF instrument

Project description:This analysis sought to evaluate the carrier proteome limits on a SCIEX 7600 ZenoTOF mass spectrometer. A 9 channel TMTPro digest standard previously described in Orsburn, et al., Nature Communcations 2022 was used. . Briefly, a K562 human peptide digest standard (Promega) and E.coli peptide standard (Waters) were resuspended in 100mM TEAB (SimpliFi) and aliquots of 10 micrograms of each were labeled with the TMTPro reagents, 126, 127n, 128n, 129n, 130n, 131n, 132n, 133n and 134 and the reactions quenched with hydroxylamine according to vendor instructions. Labeled peptides were combined to maintain and equal concentration of K562 digest in each lane by combining 2 micrograms of each. E.coli peptides were diluted to 10to5to1 in TEAB and combined with the respective lanes to result in a repeating E.coli concentration of 20% and 10% of the first channel. The combined peptides were diluted to 100ng/uL total concentration and analyzed on a SCIEX 7600 ZenoTOF instrument coupled to a Waters H Class microflow UHPLC. A 60 minute gradient was used at a flow rate of 5 uL/min using a Phenomenex column. A top 10 data dependent method was used for all analysis. The resulting output files were converted to MGF using the ProteoWizard software and the MGF files were processed in Proteome Discoverer 2.4SP1 using a 15ppm MS1 and 0.03 Da MS/MS tolerance window. Static carbamidomethylation of cysteine and TMTPro tags on lysine and peptide N-termini were used as well as dynamic modifications of methionine oxidation to search against a combination of the SwissProt Human and E.coli FASTA. The cRAP database was used for contaminant identification.

2024-02-08 | MSV000094044 | MassIVE

Metabolomics and lipidomic analysis of SLC25A22 knockdown PANC1 cells

Project description:The global metabolomics and non-targeted lipidomic analysis to detect the changes following the depletion of SLC25A22 in PANC1 cells

2023-03-08 | PXD040701 |

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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