Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantitative and In-Depth Survey of the Isotopic Abundance Distribution Errors

ABSTRACT: Quantitative and In-Depth Survey of the Isotopic Abundance Distribution Errors in Shotgun Proteomics

ORGANISM(S): Homo Sapiens

SUBMITTER: Yunping Zhu

PROVIDER: PXD008428 | iProX | Wed Dec 06 00:00:00 GMT 2017

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ZY_UPS2_A1_load.raw	Raw
	ZY_UPS2_A2_load.raw	Raw
	ZY_UPS2_A3_load.raw	Raw
	ZY_UPS2_B1_load.raw	Raw
	ZY_UPS2_B2_load.raw	Raw

Items per page:

1 - 5 of 36

Publications

Quantitative and In-Depth Survey of the Isotopic Abundance Distribution Errors in Shotgun Proteomics.

Chang Cheng C Zhang Jiyang J Xu Changming C Zhao Yan Y Ma Jie J Chen Tao T He Fuchu F Xie Hongwei H Zhu Yunping Y

Analytical chemistry 20160620 13

Accuracy is an important metric when mass spectrometry (MS) is used in large-scale quantitative proteomics research. For MS-based quantification by extracting ion chromatogram (XIC), both the mass and intensity dimensions must be accurate. Although much research has focused on mass accuracy in recent years, less attention has been paid to intensity errors. Here, we investigated signal intensity measurement errors systematically and quantitatively using the natural properties of isotopic distribu ...[more]

PMID: 27266261

Similar Datasets

Abundance of Legionellales

Project description:Abundance, diversity and distribution of Legionellales in wet environments in Sweden

| PRJEB26992 | ENA

Sequencing Facilitates Quantitative Analysis of Wild Type and d5rf mutant Transcriptomes

Project description:To gain insight into the biological role of D5RF in plants, we conducted a comprehensive survey of global gene expression employing high throughput-RNA sequencing to quantify the variations in transcript abundance between wild-type Columbia-0 (Col-0) and d5rf.

2020-10-22 | GSE155112 | GEO

Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance

2014-05-01 | GSE52801 | GEO

Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance

Project description:Recent studies have reported that competitive endogenous RNAs (ceRNAs) can act as sponges for a miRNA through their binding sites and that changes in ceRNA abundances from individual genes can modulate the miRNA’s activity. Consideration of this hypothesis would benefit from knowing the quantitative relationship between a miRNA and its endogenous target sites. Here, we altered intracellular target-site abundance through expression of a miR-122 target in hepatocytes and livers, and analyzed the effects on miR-122 target genes. Target repression was released in a threshold-like manner at high target-site abundance (≥1.5x10^5 added target sites per cell), and this threshold was insensitive to the effective levels of the miRNA. Furthermore, in response to extreme metabolic liver disease models, global target-site abundance of hepatocytes did not change sufficiently to affect miRNA-mediated repression. Thus, modulation of miRNA target abundance is unlikely to cause significant effects on gene expression and metabolism through a ceRNA effect. Seventeen mRNA profiles were generated of 1) primary hepatocytes of mice expressing variable levels of a recombinant Adenovirus expressing the transcript of AldolaseA (Ad-AldoA), containing either 1 or 3 sites matching miR-122 or a mutated miR-122 site (no site), 2) primary hepatocytes derived from mice treated with Antagomir-122 (treatment group) or Antagomir-122mm (control group), 3) livers originating of a genetic model (Ldlr deficient mice) causing severe pathological changes in cholesterol metabolism, 4) livers of mice perfused with Insulin or PBS, and 5) livers of mice fed a high-fat or chow diet; most samples were sequenced in duplicate or triplicate by an Illumina HiSeq 2000. One small RNA profile was also generated from livers of mice fed a chow diet by Solexa sequencing.

2014-05-01 | E-GEOD-52801 | biostudies-arrayexpress

In depth proteome profiling of Cumin by LTQ-Orbitrap Velos mass spectrometer

Project description:A shotgun proteomic approach was used to obtain comprehensive dataset of cumin proteins. For this purpose we applied a one dimensional electrophoresis coupled with high resolution mass spectrometry. The first step in our proteome analysis strategy, we evaluate different extraction methods, based on differential solubility of protein. Among those methods, Readyprep protein extraction kit provide high purity of protein extract, gave higher protein yield and typically good resolution of protein bands on one dimensional gel electrophoresis. Further nanoLC-MS/MS analysis by state-of-the-art linear ion trap (LTQ)-Orbitrap Velose mass spectrometer resulted in identification of very high number proteins. Bioinformatics analysis provide functional distribution of identified protein. To our knowledge, this is the first study aimed for in depth study of cumin proteome.

2022-02-28 | PXD006425 | Pride

High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq

Project description:Measurements of cellular tRNA abundance are hampered by pervasive blocks to cDNA synthesis at modified nucleosides and the extensive similarity among tRNA genes. We overcome these limitations with modification-induced misincorporation tRNA sequencing (mim-tRNAseq), which combines a workflow for full-length cDNA library construction from mature tRNA with a simple-to-use computational analysis toolkit. Our method accurately captures tRNA abundance and modification status in multiple eukaryotes and is applicable to any organism with a known genome.

2021-02-12 | GSE152621 | GEO

cercozoa soil depth

Project description:Distinct communities of Cercozoa at different soil depth in a temperate agricultural field

| PRJEB30791 | ENA

Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing

Project description:Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing

| PRJEB55684 | ENA

Depth Distribution of Ammonia Oxidation Rates and Ammonia-Oxidizer Community Composition in the Sargasso Sea

Project description:Depth Distribution of Ammonia Oxidation Rates and Ammonia-Oxidizer Community Composition in the Sargasso Sea

| PRJNA179550 | ENA

Evaluating the Impact of Sequencing Depth on Transcriptome Profiling in Human Adipose

Project description:Recent advances in RNA sequencing (RNA-Seq) have enabled the discovery of novel transcriptomic variations that are not possible with traditional microarray-based methods. Tissue and cell specific transcriptome changes during pathophysiological stress, in disease cases versus controls and in response to therapies are of particular interest to investigators studying cardiometabolic diseases. Thus, knowledge on the relationships between sequencing depth and detection of transcriptomic variation is needed for designing RNA-Seq experiments and for interpreting results of analyses. Using deeply sequenced RNA-Seq data derived from adipose of a healthy individual before and after systemic administration of endotoxin (LPS), we investigated the sequencing depths needed for studies of gene expression and alternative splicing (AS). We found that to detect expressed genes and AS events, ~100 million (M) filtered reads were needed. However, the requirement on sequencing depth for the detection of LPS modulated differential expression (DE) and differential alternative splicing (DAS) was much higher. To detect 80% of events, ~300M filtered reads were needed for DE analysis whereas at least 400M filtered reads were necessary for detecting DAS. Although the majority of expressed genes and AS events can be detected with modest sequencing depths (~100M filtered reads), the estimated gene expression levels and exon/intron inclusion levels were less accurate. We report the first study that evaluates the relationship between RNA-Seq depth and the ability to detect DE and DAS in human adipose. Our results suggest that a much higher sequencing depth is needed to reliably identify DAS events than for DE genes. Random sampling the RNA-seq data in different depth for gene and alternative-splicing analysis

2013-07-12 | E-GEOD-46323 | 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