Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A comprehensive LFQ benchmark dataset to validate data analysis pipelines on modern day acquisition strategies in proteomics

ABSTRACT: A comprehensive LFQ benchmark dataset to validate data analysis pipelines on modern day acquisition strategies in proteomics using SCIEX TripleTOF5600 and 6600+, Orbitrap QE-HFX, Waters Synapt GS-Si and Synapt XS and Bruker timsTOF Pro.

INSTRUMENT(S): timsTOF Pro, TripleTOF 5600, TripleTOF 6600, Synapt MS, Q Exactive HF

ORGANISM(S): Homo Sapiens (human) Escherichia Coli Candida Albicans (yeast)

SUBMITTER: Yasset Perez-Riverol

LAB HEAD: Maarten Dhaenens

PROVIDER: PXD028735 | Pride | 2022-02-14

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw	Raw
	LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw	Raw
	LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw	Raw
	LFQ_Orbitrap_AIF_Condition_A_Sample_Beta_01.raw	Raw
	LFQ_Orbitrap_AIF_Condition_A_Sample_Beta_02.raw	Raw

Items per page:

1 - 5 of 844

Similar Datasets

A comprehensive LFQ benchmark dataset to validate data analysis pipelines on modern day acquisition strategies in proteomics

Project description:A comprehensive LFQ benchmark dataset to validate data analysis pipelines on modern day acquisition strategies in proteomics using SCIEX TripleTOF5600 and 6600+, Orbitrap QE-HFX, Waters Synapt GS-Si and Synapt XS and Bruker timsTOF Pro.

2024-10-23 | MSV000096179 | MassIVE

Optimizing RNA Extraction Methods for High Throughput Transcriptome Sequencing of Fresh Frozen and Formalin-Fixed Paraffin-Embedded Cardiac Tissues Specimens

Project description:In this study, the efficiency of four RNA extraction methods was compared on 23 FFPE cardiac tissue specimens. The Qiagen AllPrep DNA/RNA FFPE kit (Method QP), Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization (Method QE), CELLDATA RNAstorm 2.0 FFPE RNA Extraction kit (Method BP) and CELLDATA RNAstorm 2.0 FFPE RNA Extraction Kit with protocol modifications on the lysis step (Method BL). In comparing RNA quality metrics across FFPE RNA extract, nucleic acids extracted with Method QE and QP had the highest RNA yield. However, Method QE outperformed Method QP as more extract from Method QE had DV 200 values above 30%. Both method BL and BP produced a similar range of RNA purity and yield but more extract from Method BL had DV 200 values above 30% compared to Method BP. When accessing distribution value, Method BL outperformed Methods BP, QE, and QP as more extracts from Method BL had DV 200 values above 30% (16/23 samples) compared to other methods (PDV200<0.001; Kruskal-Wallis). However, method QE outperformed other methods in terms of RNA yield. The sequencing performance of RNA extracts from Method QE and Method BL was further tested on 8 matching samples with high RNA yield and high DV200 value respectively. RNA extracts from Method QE which yielded the highest RNA quantity among all methods exhibited comparable sequencing performance to extract obtained through Method BL, which yielded extract with high DV200 value. This study suggests that the DV200 and RNA yield are both reliable pre-analytic metrics in determining a suitable method for successful transcriptome sequencing of FFPE samples and have important implications for future studies exploring transcriptome sequencing of FFPE cardiac specimens.

2024-05-23 | GSE267659 | GEO

Benchmarking label-free quantification based on data-independent acquisition (DIA) workflows

Project description:Label-free quantification based on data-independent acquisition (DIA) workflows is increasingly popular. Several software tools have been recently published or are commercially available. The present study focuses on the critical evaluation of three different software packages (Progenesis, synapter and ISOQuant) supporting ion-mobility enhanced DIA data. In order to benchmark the label-free quantification performance of the different tools, we generated two hybrid proteome samples of defined quantitative composition containing tryptically digested proteomes of three different species (mouse, yeast, E.coli). This model data set simulates complex biological samples containing large numbers of both unregulated (background) proteins as well as up- and down-regulated proteins with exactly known ratios between samples. We determined the number and dynamic range of quantifiable proteins and analyzed the influence of applied algorithms (retention time alignment, clustering, normalization, etc.) on the variation of reported protein quantities between technical replicates.

2017-04-06 | PXD001240 | Pride

Discovery of potential early colorectal cancer biomarker

Project description:Differential analysis of proteomes originated from early lesion of colorectal cancer and colon control tissue using FFPE-FASPTM and Label free analysis using 2DnanoUPLC separation before analysis on a qTOF synapt HDMS G2 using ion mobility as supplementary separation dimension

2017-03-28 | PXD005735 | Pride

RNA-seq mouse development

Project description:The genetic code is an abstraction of how mRNA codons and tRNA anticodons molecularly interact during protein synthesis; the stability and regulation of this interaction remains largely unexplored. Here, we quantitatively characterized the expression of mRNA and tRNA genes across developing mouse tissues. Substantial fractions of both gene sets dynamically change expression from early organogenesis to adult tissues. mRNA codon pools are highly stable over development and reflect the genomic background; in contrast, changes in transcription at specific tRNA genes are coordinated across anticodon families to produce a stable isoacceptor output. During development, the pools of mRNA codons and tRNA anticodons are invariant and highly correlated, revealing a stable molecular interaction interlocking transcription and translation.

2014-08-08 | E-MTAB-2328 | biostudies-arrayexpress

QE soil

Project description:QE soil Raw sequence reads

| PRJNA414938 | ENA

Targeted Feature Detection and Extraction

Project description:Missed identifications of peptides in data-dependent acquisition (DDA) proteomics experiments is an obstacle n the precise determination of which proteins are present in a sample and their relative abundance. Efforts pular analysis workfl raw data to transfer a pehtiraw identifiher. Another approach ipeptide identifictatioimpute peptide idich they were missing.Wen which they were missing.We propoted xtractio called targeted extractio called targeted extractio called targeted extxactio c called targeted eractio called targeted extractio called targeted extraugh which prees t t in a run. The modeeiseetween obdentifieference library o pep from muliseetween obdentifieference library o pep from mulise the risk of drawing nimise the risk of drawing nimise the risk of dra drg nim nimihe the risk of drawing niminimise the risk of drawiies, oate of false discs Verechgtperforms the poe (FDR)tios of decoys as targtperforms the poe (FDR)tios of decoys as targtperforms the poe (FDR)tios of decoys as targtperforms the poe (FDR)tios of decoys as targtperforms the popular anand MSFraggt will be a vaprabeomics ribution to the proteomics ribution to the proteomics ribution to the proteomics ribution to the proteomics ribution to the proteomics ribution to the proteomics ribution to the proteomics toolbox for protein quantification.

2022-03-07 | PXD030706 | Pride

Faustovirus global proteome - Faustovirus, an asfarvirus-related new lineage of giant viruses infecting amoebae

Project description:Global proteome study of two protein extracts of purified Faustovirus, using a bi dimensionnal nanoLC fractionnation combined to a Synapt G2 Si HDMSe monitoring enabling ion mobility

2015-04-22 | PXD001858 | Pride

Multiplexed Quantitative Analyses Using Data-Dependent Acquisition Without Dynamic Exclusion for trace sample analysis

Project description:In this project, we applied our recently developed turboDDA method in the analysis of low amount of sample and iTRAQ labeled trace sample. Compared with standard data-ependent acquisition approach with dynamic exclusion, we detected improvment in spectral purity and quantification accuracy.

2024-01-26 | PXD042252 | Pride

Tupavirus global proteome - Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere

Project description:Global proteome study of protein extracts of purified Tupavirus, using a bidimensionnal nanoLC fractionnation combined to a Synapt G2 Si HDMSe monitoring enabling ion mobility

2018-10-24 | PXD007583 | Pride

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