Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Modifying Chromatography Conditions for Improved Unknown Feature Identification in Untargeted Metabolomics

ABSTRACT: Project represents an effort to modify chromatographic conditions for improved compound identification in untargeted metabolomics. Two different modes of chromatograph (HILIC and RPLC) and multiple run conditions (sample loading, gradient duration, iterative acquisition) were evaluated. All relevant data from different conditions are contained within the raw data archive file attached to this submission. Metadata associated with this Metabolomics Workbench submission reflects only the manually reviewed identifications obtained using modified HILIC conditions. See protocol file Mod_vs_Con_Chrom_IDs_Protocol.pdf for details.

ORGANISM(S): Human Homo Sapiens

TISSUE(S): Blood

SUBMITTER: Brady Anderson

PROVIDER: ST001753 | MetabolomicsWorkbench | Thu Sep 09 00:00:00 BST 2021

REPOSITORIES: MetabolomicsWorkbench

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	mwtab	Other

Items per page:

1 - 1 of 1

Similar Datasets

GNPS Metabolomics Workbench ST001753 - GNPS Modifying Chromatography Conditions for Improved Unknown Feature Identification in Untargeted Metabolomics

Project description:Project represents an effort to modify chromatographic conditions for improved compound identification in untargeted metabolomics. Two different modes of chromatograph (HILIC and RPLC) and multiple run conditions (sample loading, gradient duration, iterative acquisition) were evaluated. All relevant data from different conditions are contained within the raw data archive file attached to this submission. Metadata associated with this Metabolomics Workbench submission reflects only the manually reviewed identifications obtained using modified HILIC conditions. See protocol file "Mod_vs_Con_Chrom_IDs_Protocol.pdf" for details.

2021-11-20 | MSV000088420 | GNPS

Project description:Test fast5 file submission

| PRJNA511553 | ENA

The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (expression data)

Project description:We established whether partner transcription factor binding, chromatin structure, or gene expression is compromised upon loss of partner factors cdx2 or hnf4a in mouse intestinal villi This metadata file describes the gene expression componant of that data

2013-02-05 | GSE34567 | GEO

The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (ChIP-seq data)

Project description:We established whether partner transcription factor binding, chromatin structure, or gene expression is compromised upon loss of partner factors cdx2 or hnf4a in mouse intestinal villi. This metadata file describes the ChIP-seq componant of that data

2013-02-05 | GSE34566 | GEO

Test MassIVE Dataset for Metadata and License

Project description:Test dataset with example metadata and license file. Non-commercial license is granted to use this data. Attribution is required. Please see the attached license file prior to using the data

2024-03-28 | MSV000094430 | MassIVE

ThinPrep Cervical Smear iTRAQ LC-MS/MS

Project description:The protein content from ThinPrep cervical smear specimens was purified with TCA precipitation. The protein pellets were dissolved and protein concentration was measured with the Bradford assay. 100 ug of protein for each sample were reduced with TCEP, cysteines were blocked with MMTS and finally digested overnight with trypsin. The resultant peptides were labeled with the iTRAQ 8plex reagents and after mixing were subjected to off-line high pH C18 fractionation. The peptide fractions were further analyzed with low pH C18 LC-Orbitrap Elite HCD MS/MS (MS resolution 120,000, top 10 precursors, isolation width 1.2 m/z, 100 min gradient method). Protein Identification was performed using Proteome Discoverer 1.3 software. SEQUEST node included prec. mass tolerance: 10 ppm, fragment mass tolerance 0.5 Da, iTRAQ8plex Nterm and K,Y static modification, Methylthio static modification, Phospho S variable modification, Oxidation M variable modification, Deamidation N,Q variable modification. All spectra were search against a Uniprot fasta file containing all reviewed Human entries and all reviewed and un-reviewed human papillomavirus entries. Peptide and PTM validation was performed with Percolator and PhosphoRS nodes respectively. Protein quantitation was performed with the Reporter Ions Quantifier node.

2013-05-09 | PXD000109 | Pride

Profiling of a high mannose-type N-glycosylated lipase using hydrophilic interaction chromatography-mass spectrometry

Project description:We report the use of hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) to profile intact glycoform distributions of high mannose-type N-glycosylated proteins, using an industrially produced fungal lipase for the food industry as an example. We compared these results with conventional reversed phase LC-MS (RPLC-MS) and sodium dodecyl sulfate–polyacrylamide gel-electrophoresis (SDS-PAGE). HILIC appeared superior in resolving lipase heterogeneity, facilitating mass assignment of N-glycoforms and sequence variants. Fractions representing the four main HILIC elution bands for lipase were subjected to SDS-PAGE confirming that HILIC retention increased with the number of glycosylation sites (0-3) occupied. Additional bottom-up proteomic analysis of the fractions enabled the identification of the most abundant glycosylation sites. Compared to RPLC-MS, HILIC-MS provided a stronger reduction of the sample complexity delivered to the mass spectrometer, facilitating the assignment of the masses of glycoforms and sequence variants as well as increasing the number of glycoforms detected (69 more proteoforms, 177% increase). The HILIC-MS method required relatively short analysis time (< 30 min), in which over 100 glycoforms were distinguished. We suggest that HILIC-MS can be used to characterize bioengineering processes aimed at steering protein glycoform expression as well as to check the consistency of product batches.

2020-05-04 | PXD016215 | Pride

Online Weak Cation Exchange-HILIC × Reversed Phase LC UVPD-HRMS of intact HeLa Histones

Project description:Intact HeLa core Histones were analyzed using an online two-dimensional liquid chromatographic separation as well as one dimensional LC (RPLC and WCX-HILIC) coupled with UVPD-MS

2018-09-19 | PXD008978 | Pride

Two-dimensional low-flow liquid-chromatography setup for shotgun proteomics

Project description:Development of low-flow liquid-chromatography setup by combining hydrophylic interaction liquid chromatography (HILIC) and reversed phase liquid chromatography (RPLC) and coupled with a high resolution mass spectrometer.

2021-03-29 | PXD022330 | Pride

ATR in C. jejuni

Project description:Microarrays were used to identify genes that participate in the acid responce tolerance of C. jejuni. Three biological replicates of two different conditions (pH 5.5 and 7). Two slides and every slide contained three arrays- see attached additional file.

2015-07-01 | E-MEXP-3835 | biostudies-arrayexpress

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