Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spike-in comparison - Data processing has major impact on the outcome of quantitative label-free LC-MS analysis

ABSTRACT: Synthetic peptides were spiked in at different levels in a digested cell lysate from Streptococcus pyogenes

INSTRUMENT(S): LTQ Orbitrap XL ETD

ORGANISM(S): Streptoccous Pyogenes

SUBMITTER: Fredrik Levander

LAB HEAD: Fredrik Levander

PROVIDER: PXD001091 | Pride | 2014-11-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	130124_dilA_10_01.mgf	Mgf
	130124_dilA_10_01.raw	Raw
	130124_dilA_10_02.mgf	Mgf
	130124_dilA_10_02.raw	Raw
	130124_dilA_10_03.mgf	Mgf

Items per page:

1 - 5 of 286

Publications

Data processing has major impact on the outcome of quantitative label-free LC-MS analysis.

Chawade Aakash A Sandin Marianne M Teleman Johan J Malmström Johan J Levander Fredrik F

Journal of proteome research 20141126 2

High-throughput multiplexed protein quantification using mass spectrometry is steadily increasing in popularity, with the two major techniques being data-dependent acquisition (DDA) and targeted acquisition using selected reaction monitoring (SRM). However, both techniques involve extensive data processing, which can be performed by a multitude of different software solutions. Analysis of quantitative LC-MS/MS data is mainly performed in three major steps: processing of raw data, normalization, ...[more]

PMID: 25407311

Similar Datasets

Reanalysis of spike-in samples

Project description:Two samples in submission PXD001091 were reanalysed 22 months later on the same instrument.

2015-04-20 | PXD002037 | Pride

Expression analysis of Streptococcus pyogenes NZ131 serR-

Project description:Whole genone expression profile comparing wild-type NZ131 to serR deletion mutant, grown in C-medium Mutants and interpretation are described further in the manuscript to be submitted: LaSarre and Federle, 2010. Title: Regulation and Consequence of Serine Catabolism in Streptococcus pyogenes. A two chip study using total RNA recovered from three separate wild-type cultures of Streptococcus pyogenes NZ131 and three separate mutant cultures of Streptococcus pyogenes NZ131 seR-, pooled following RNA extraction

2010-11-15 | E-GEOD-24860 | biostudies-arrayexpress

Gene expression of GidA mutant Streptococcus pyogenes

Project description:In Streptococcus pyogenes, mutation of GidA results in avirulence despite the same growth rate as the wild type. To understand the basis of this effect, global transcription profiling was conducted. Keywords: Wild type vs. GidA mutant Streptococcus pyogenes

2008-01-10 | GSE9678 | GEO

Counteractive balancing of transcriptome expression involving CodY and CovRS in Streptococcus pyogenes

Project description:Streptococcus pyogenes (group A Streptococcus, GAS) responds to environmental changes in a manner that results in an adaptive regulation of the transcriptome. Global transcriptional regulators are able to integrate important extracellular and intracellular information and are responsible for modulation of the transcriptional network. The roles of several global transcriptional regulators in adaptation and virulence gene expression have been described. In this study we used microarray to investigate the regulatory roles of CodY and CovRS played in Streptococcus pyogenes. keywords: genetic modification Streptococcus pyogenes NZ131 wild-type cells, ΔcodY, ΔcovRS and ΔcodYcovRS strains were grown in C-medium until mid-exponential phase or early-stationary phase. The transcriptional profile of the whole genome was examined with microarray.

2011-03-01 | E-GEOD-26590 | biostudies-arrayexpress

Comparison of gene expression changes in Streptococcus pyogenes in the presence of zinc

Project description:Manuscript title: Zinc disrupts central carbon metabolism and capsule biosynthesis in Streptococcus pyogenes. Macrophages and neutrophils release free zinc to eliminate phagocytosed bacterial pathogens. The study investigates the effect of how zinc toxicity affects Streptococcus pyogenes. Therefore, a microarray analysis was performed in S. pyogenes cells to determine gene expression changes when exposed to high levels of zinc. We discovered that a pathway involved in tagatose-6-phosphate metabolism was upregulated when the cells are under zinc stress.

2015-11-30 | GSE63436 | GEO

Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pyogenes

Project description:The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to Streptococcus pyogenes strains 5448, SP444, HKU419, PS003 and PS006.

2021-07-05 | PXD016913 | Pride

Counteractive balancing of transcriptome expression involving CodY and CovRS in Streptococcus pyogenes

2011-03-01 | GSE26590 | GEO

Identification of Distinct Impacts of CovS Inactivation on the Transcriptome of Acapsular Group A Streptococci

Project description:To determine the impact of CovS inactivation in acapsular GAS (Streptococcus pyogenes) strains

2023-04-25 | GSE230158 | GEO

Multiple roles of RNase Y in Streptococcus pyogenes mRNA metabolism

Project description:Streptococcus pyogenes (Group A streptococcus, GAS) is an important human pathogen that causes a variety of infectious diseases and sequelae. Recent studies showed virulence factor expression was controlled at multiple levels, including the post-transcriptional regulation. In this study, we examined the global half-lives of S. pyogenes mRNAs and explored the role RNase Y played in mRNA metabolism with microarray analysis. key word: genetic modification

2013-02-01 | GSE40198 | GEO

Insert in CovS Gene Distinguishes a Pharyngeal and a Blood Isolate of Streptococcus pyogenes Found in the Same Individual.

Project description:Expression of the extensive arsenal of virulence factors by Streptococcus pyogenes are controlled by many regulators, of which covR/S is one of the best characterized and can influence ~15% of the genome. Animal models have established that mutants of CovR/S arise spontaneously in vivo resulting in highly invasive organisms. We analyzed a pharyngeal and a blood isolate of S. pyogenes recovered from the same individual 13 days apart. The two isolates varied in many phenotypic properties including speB production, which were reflected in transcriptome analyses. Pulsed field gel electrophoresis, multilocus sequence typing, and partial sequencing of some key genes failed to show any differences except for an 11-base insert in the covS gene in the blood isolate. These results showing that pharyngeal and blood isolates from a single individual which differ by a simple insertion, provide evidence for the model that regulatory gene mutations allow S. pyogenes to invade different niches in the body. A chip study using total RNA recovered from two separate wild-type cultures of group A Streptococcus, Streptococcus pyogenes UH322 and UH328. Each chip measures the expression level of 1865 genes replicated twice from 7 fully sequenced strains of Streptococcus pyogenes (M1_GAS NC_002737; MGAS10394 NC_006086; MGAS315 NC_004070; MGAS5005 NC_007297; MGAS6180 NC_007296; MGAS8232 NC_003485; SSI-1 NC_004606 with fourteen 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

2010-05-01 | E-GEOD-21316 | 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