Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

2 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The MS data for precision evaluation of absolute quantification algorithms

ABSTRACT: Human embryonic kidney (HEK) cells 293 are analyzed by two state-of-the-art MS instruments (Thermo Orbitrap Fusion and Q Exactive HF) in quadruplicate for precision evaluation.

ORGANISM(S): Homo Sapiens

SUBMITTER: Yunping Zhu

PROVIDER: PXD009720 | iProX | Tue May 08 00:00:00 BST 2018

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

LFAQ: Toward Unbiased Label-Free Absolute Protein Quantification by Predicting Peptide Quantitative Factors.

Chang Cheng C Gao Zhiqiang Z Ying Wantao W Fu Yan Y Zhao Yan Y Wu Songfeng S Li Mengjie M Wang Guibin G Qian Xiaohong X Zhu Yunping Y He Fuchu F

Analytical chemistry 20181221 2

Mass spectrometry (MS) has become a predominant choice for large-scale absolute protein quantification, but its quantification accuracy still has substantial room for improvement. A crucial issue is the bias between the peptide MS intensity and the actual peptide abundance, i.e., the fact that peptides with equal abundance may have different MS intensities. This bias is mainly caused by the diverse physicochemical properties of peptides. Here, we propose an algorithm for label-free absolute prot ...[more]

PMID: 30525483

Similar Datasets

Systematic comparison of RNA-seq pipelines for absolute and relative gene expression quantification

Project description:At present, it is admitted that RNA-seq is a more powerful and adaptable technique than hybridization arrays. Nevertheless, as RNA-seq needs a more complex data analysis, it has generated a lot of research on algorithms and workflows. This has resulted in an exponential increase of the options at each step of the analysis. Consequently, there is no clear consensus on the appropriate algorithms and pipelines that should be used to analyse RNA-seq data. In the present study, 192 pipelines on 18 samples from 2 human cell lines were evaluated. Absolute gene expression quantification was assessed by non-parametric statistics to measure precision and accuracy. Relative gene expression performance was estimated testing 19 differential expression methods. These results were contrasted in parallel with the microarray HTA 2.0 data from Affymetrix using the same set of samples. All procedures were validated by qRT-PCR on 32 genes in all samples. In addition, this study proposes a new statistical approach for precision and accuracy evaluation on real RNA-seq data. It also weights up the advantages and disadvantages of the algorithms and pipelines tested and gives a guide to select the appropriate pipeline to analyse RNA-seq and microarray data.

2021-02-28 | GSE116291 | GEO

The MS data for accuracy evaluation of absolute quantification algorithms

Project description:The DDA and DIA data for accuracy evaluation of absolute quantification algorithms.

2018-05-08 | PXD009719 | iProX

Evaluation of digital PCR for absolute RNA quantification.

Project description: Not available

| S-EPMC3779174 | biostudies-literature

Absolute quantification of miRNAs

2009-10-27 | GSE15835 | GEO

Performance evaluation of the Q Exactive HF-X for shotgun proteomics

Project description:Performance evaluation of the Q Exactive HF-X for shotgun proteomics

2017-11-30 | PXD006932 | Pride

Absolute quantification of miRNAs

Project description:MicroRNAs (miRNAs) have been shown to play an important role in many different cellular, developmental, and physiological processes. Accordingly, numerous methods have been established to identify and quantify miRNAs. The shortness of miRNA sequence results in a high dynamic range of melting temperatures and, moreover, impedes a proper selection of detection probes or optimized PCR primers. While miRNA microarrays allow for massive parallel and accurate relative measurement of all known miRNAs, they have so far been less useful as an assay for absolute quantification. Here, we present a microarray based approach for global and absolute quantification of miRNAs. The method relies on an equimolar pool of about 1000 synthetic miRNAs of known concentration which is used as an universal reference and labeled and hybridized in a dual colour approach on the same array as the sample of interest. Each single miRNA is quantified with respect to the universal reference outbalancing bias related to sequence, labeling, hybridization or signal detection method. We demonstrate the accuracy of the method by various spike in experiments. Further, we quantified miRNA copy numbers in liver samples and CD34(+)CD133(-) hematopoietic stem cells. Total liver RNA was mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3â ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool (n = 6). The synthetic miRNA pool consisted of 2.5 fmol of each of 891 non redundant miRNAs sequences and miRControl 3 sequences. The array data was normalized by calculating the median of the miRControl 3 present in the liver and UR sample. The miRNA amount was calculated with respect to the corresponding miRNA in the UR.

2010-06-20 | E-GEOD-15835 | biostudies-arrayexpress

Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae

Project description:Computing absolute protein abundances using mass spectrometry (MS) is a widely used technique in quantitative biology. An important and often overlooked aspect in this methodology is to assess technical reproducibility, i.e. how precise are predictions of abundance when we use the instrument on repeated occasions to measure the same sample. Here, we present a proteomics dataset of Saccharomyces cerevisiae with both biological and inter-run technical triplicates, which we use to analyze both accuracy and precision of the MS instrument. We also investigate how we can improve the quality of predictions by using 4 alternative methods for estimating absolute protein abundance starting from MS intensities. We show that using a simple normalization and rescaling approach performs equally accurate, but much more precise, than methods that rely on external standards. Furthermore, we show that technical reproducibility is significantly lower than biological reproducibility for all the evaluated methods. The results presented here serve as a benchmark for assessing the best way of interpreting MS results to compute protein abundances, and as a consideration of the limitations of the technique when interpreting results.

2020-04-09 | PXD011725 | Pride

Absolute quantification of miRNAs

Project description:Absolute quantification of miRNAs

| PRJNA116765 | ENA

Comparative evaluation of label-free quantification strategies

Project description:Comparative evaluation of label-free quantification strategies

2020-05-27 | PXD019408 | iProX

Molecular Characterization of a Precision-Cut Rat Liver Slice Model for the Evaluation of Anti-Fibrotic Compounds

Project description:Precision-cut liver tissue slice (PCLS) contains all major cell types of the liver parenchyma and preserves the original cell-cell and cell-matrix contacts. It represents a promising ex vivo model to study liver fibrosis and test the anti-fibrotic effect of experimental compounds in a physiologic environment. In this study using RNAquencing we demonstrated that various pathways functionally related to fibrotic mechanisms were dysregulated in PCLSs derived from rats subjected to bile duct ligation. The Alk5 inhibitor SB525334, nintedanib and sorafenib each reversed a subset of genes dysregulated in fibrotic PCLSs and of those genes we identified 608 genes whose expression was reversed by all three compounds. These genes define a molecular signature characterizing many aspects of liver fibrosis pathology and its attenuation in the model. A panel of 12 genes and 4 secreted biomarkers including procollagen I, HA, IGFBP5 and WISP1, were further validated as efficacy endpoints for the evaluation of anti-fibrotic activity of experimental compounds. Finally, we showed that blockade of αV integrins with a small molecule inhibitor attenuated the fibrotic phenotype in the model. Overall, our results suggest that the rat fibrotic PCLS model may represent a valuable system for target validation and to determine the efficacy of experimental compounds.

2018-10-04 | GSE120804 | GEO

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