Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PASS00589 - Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues

ABSTRACT: The data set repersents a fair comparison of shotgun proteomics with HRM (swath type DIA). Additionally, a human liver microtissue was profiled with HRM.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Lukas Reiter

PROVIDER: MSV000081828 | MassIVE | Tue Dec 19 10:10:00 GMT 2017

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Publications

Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues.

Bruderer Roland R Bernhardt Oliver M OM Gandhi Tejas T Miladinović Saša M SM Cheng Lin-Yang LY Messner Simon S Ehrenberger Tobias T Zanotelli Vito V Butscheid Yulia Y Escher Claudia C Vitek Olga O Rinner Oliver O Reiter Lukas L

Molecular & cellular proteomics : MCP 20150227 5

The data-independent acquisition (DIA) approach has recently been introduced as a novel mass spectrometric method that promises to combine the high content aspect of shotgun proteomics with the reproducibility and precision of selected reaction monitoring. Here, we evaluate, whether SWATH-MS type DIA effectively translates into a better protein profiling as compared with the established shotgun proteomics. We implemented a novel DIA method on the widely used Orbitrap platform and used retention- ...[more]

PMID: 25724911

Similar Datasets

Reprocessed dataset with Skyline Batch: Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues

Project description:The data set represents a fair comparison of shotgun proteomics with HRM (swath type DIA). Additionally, a human liver microtissue was profiled with HRM. REPROCESSING METHODS: Skyline Batch is a newly developed Windows forms application that enables easy and consistent reprocessing of data with Skyline. Skyline has made previous advances in this direction; however, none enable seamless automated reprocessing of local and remote files. Skyline keeps a log of all the steps that were taken in the document; however, reproducing these steps takes time and allows room for human error. Skyline also has a command-line interface, enabling it to be run from a batch script, but using the program in this way requires expertise in editing these scripts. By formalizing the workflow of a highly used set of batch scripts into an intuitive and powerful user interface, Skyline Batch can reprocess data stored in remote repositories just by opening and running a Skyline Batch configuration file. When run, a Skyline Batch configuration downloads all necessary remote files and then runs a four-step Skyline workflow. By condensing the steps needed to reprocess the data into one file, Skyline Batch gives researchers the opportunity to publish their processing along with their data and other analysis files. These easily run configuration files will greatly increase the transparency and reproducibility of published work. Skyline Batch is freely available at https://skyline.ms/batch.url.

2021-11-12 | PXD029663 | panorama

Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues.

Project description:The data-independent acquisition (DIA) approach has recently been introduced as a novel mass spectrometric method that promises to combine the high content aspect of shotgun proteomics with the reproducibility and precision of selected reaction monitoring. Here, we evaluate, whether SWATH-MS type DIA effectively translates into a better protein profiling as compared with the established shotgun proteomics. We implemented a novel DIA method on the widely used Orbitrap platform and used retention-time-normalized (iRT) spectral libraries for targeted data extraction using Spectronaut. We call this combination hyper reaction monitoring (HRM). Using a controlled sample set, we show that HRM outperformed shotgun proteomics both in the number of consistently identified peptides across multiple measurements and quantification of differentially abundant proteins. The reproducibility of HRM in peptide detection was above 98%, resulting in quasi complete data sets compared with 49% of shotgun proteomics. Utilizing HRM, we profiled acetaminophen (APAP)(1)-treated three-dimensional human liver microtissues. An early onset of relevant proteome changes was revealed at subtoxic doses of APAP. Further, we detected and quantified for the first time human NAPQI-protein adducts that might be relevant for the toxicity of APAP. The adducts were identified on four mitochondrial oxidative stress related proteins (GATM, PARK7, PRDX6, and VDAC2) and two other proteins (ANXA2 and FTCD). Our findings imply that DIA should be the preferred method for quantitative protein profiling.

| S-EPMC4424408 | biostudies-literature

Proteomic analysis of liver cytosol and mitochondria of apoE-KO mice treated with TUG-891.

Project description:ApoE-KO mice were treated with FFAR4 agonist TUG-891 for 16 weeks. Protein abundance changes in relation to untreated control were measured in liver samples fractionated to cytosol and mitochondria by SWATH-MS.

2024-08-09 | PXD028535 | Pride

Transcriptional profile of Mouse liver after MitoCDNB application

Project description:To assess the effect of MitoCDNB on transcriptional profile of mouse liver tissue we injected mice with either vehicle (0.1 % ethanol) or 5 mg/kg of MitoCDNB. Liver was taken from both vehicle or MitoCDNB injected mice after 1 or 4 hours and the transcriptome assessed using Illumina RNASeq.

2019-04-03 | GSE117425 | GEO

Gene expression in the chronic ethanol-treated rat liver during liver regeneraiton

Project description:In this study, we analyzed the effects of chronic alcohol consumption on liver repair and regeneration after partial hepatectomy (PHx). Rats were fed a liquid diet containing 36% of total calories derived from ethanol for 5 weeks; corresponding pair-fed calorie-matched controls were fed diets in which ethanol calories were replaced either by carbohydrate or by fat. After 5 weeks, rats were subjected to 70% PHx and liver samples were collected at 1, 6 and 24h after the surgery. The excised liver samples at t=0 served as within-animal controls. We used Affymetrix Rat Gene 1.0 ST arrays to obtain global gene expression data from each liver sample (n=4 replicate rats, 72 arrays total). Gene expression was profiled in the chronic ethanol-fed (EtOH) and carbohydrate control pair-fed (CHO) liver prior to (control) and 1 h, 6 h, 12 h, and 24 h after partial hepatectomy (PHx).

2012-07-23 | E-GEOD-33785 | biostudies-arrayexpress

Quantitative data-independent acquisition glycoproteomics of sparkling wine

Project description:We developed an automated workflow that created ion libraries to analyse Sequential Window Acquisition of all THeoretical mass spectra (SWATH) Data Independent Acquisition (DIA) mass spectrometry data based on glycopeptides identified by Byonic. We applied our workflow to three pairs of experimental sparkling wines to assess the effects of aging on lees and of different yeasts strains used in Liqueur de Triage for secondary fermentation.

2020-09-18 | PXD019572 | Pride

76 human liver tissue proteomes by PCT-SWATH

Project description:Rapid proteotyping of 38 human liver tissues in duplicate using pressure-cycling technology (PCT) and SWATH mass spectrometry

2018-10-31 | PXD004873 | Pride

Transcriptional profile of Mouse liver after MitoCDNB application

Project description:Transcriptional profile of Mouse liver after MitoCDNB application

| PRJNA482096 | ENA

Gene expression in matched primary and liver metastases

Project description:We profiled primary colon cancer and liver metastatic tumours from two patients.

2020-09-16 | GSE147738 | GEO

DNA methylation profiles of liver and placenta technical replicates

Project description:We profiled DNA from liver and placenta technical replicate samples on the Illumina HumanMethylation450 BeadChip array. There technical replicates represent a single liver and a single placenta sample.

2014-02-19 | GSE52731 | GEO

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