Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human) Escherichia Coli Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Ci Wu

LAB HEAD: Shen Zhang

PROVIDER: PXD042252 | Pride | 2024-01-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20210310_iTRAQ_DE_1061_01.wiff	Wiff
	20210310_iTRAQ_DE_1061_01.wiff.scan	Wiff
	20210310_iTRAQ_DE_1061_02.wiff	Wiff
	20210310_iTRAQ_DE_1061_02.wiff.scan	Wiff
	20210310_iTRAQ_DE_1061_03.wiff	Wiff

Items per page:

1 - 5 of 31

Publications

Trace Sample Proteome Quantification by Data-Dependent Acquisition without Dynamic Exclusion.

Wu Ci C Lei Jiao J Meng Fei F Wang Xingyao X Wong Cassandra J CJ Peng Jiaxi J Lin Ge G Gingras Anne-Claude AC Ma Junfeng J Zhang Shen S

Analytical chemistry 20231130 49

Despite continuous technological improvements in sample preparation, mass-spectrometry-based proteomics for trace samples faces the challenges of sensitivity, quantification accuracy, and reproducibility. Herein, we explored the applicability of turboDDA (a method that uses data-dependent acquisition without dynamic exclusion) for quantitative proteomics of trace samples. After systematic optimization of acquisition parameters, we compared the performance of turboDDA with that of data-dependent ...[more]

PMID: 38032138

Similar Datasets

Dosage compensation mass spectrometry in platypus, chicken and mouse

Project description:Gene dosage imbalance of heteromorphic sex chromosomes (XY or ZW) exists between the sexes, and with the autosomes. Mammalian X chromosome inactivation was long thought to imply a critical need for dosage compensation in vertebrates. However, mRNA abundance measurements that demonstrated sex chromosome transcripts are neither balanced between the sexes or with autosomes in monotreme mammals or birds brought sex chromosome dosage compensation into question. This study examines transcriptomic and proteomic levels of dosage compensation in platypus and chicken compared to mouse, a model eutherian species. We analyzed mRNA and protein levels in heart and liver tissues of chicken, mouse and platypus.

2024-07-30 | PXD040182 | Pride

Peanut (Arachis hypogaea L.)-root- LC-MS/MS

Project description:The root proteomics of two cultivars differing in seed Cd accumulation, Fenghua 1 (F, low Cd cultivar) and Silihong (S, high Cd cultivar), were investigated under 0 (CK) and 2 μM Cd (Cd) conditions. The eight root proteins from two biological replicates of both peanut cultivars under Cd-free and Cd treated were obtained from iTRAQ experiments.

2019-03-19 | PXD012670 | Pride

Proteomic analysis of gynecologic cancer tissue

Project description:Using iTRAQ technology, we performed shotgun proteomics of gynecological cancer tissues, which tumor cells were captured by laser microdissection to identify biomarker candidate proteins, for gynecological cancer.

2016-04-27 | PXD001849 | Pride

Effect of deletion of htpG on global proteomic profile of M. tuberculosis H37Rv

Project description:The main objective of this study is to understand the effect of deletion of htpG on protein expression profile of M. tuberculosis H37Rv. Whole cell lysates were prepared from 4 biological replicates of the wild-type control and the ∆htpG knockout strains by bead beating in 1X PBS containing protease inhibitors and subjected to 8-plex iTRAQ.

2023-07-20 | PXD039393 | Pride

Tef (Eragrostis tef) iTRAQ-labelled protein fractions

Project description:The orphan crop, Eragrostis tef, was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants to tolerate water loss to 50% RWC before adverse effects in leaf tissues were observed. Proteomic analysis using iTRAQ mass spectrometry and appropriate database searching enabled the detection of 5727 proteins, of which 211 proteins, including a number of spliced variants, were found to be differentially regulated with imposed stress conditions. Validation of the stress-related proteins, fructose-bisphosphate aldolase (FBA), glutamine synthetase (GLN) and the protective antioxidant proteins, monodehydroascorbate reductase (MDHAR) and peroxidase (POX), using immunodetection and enzymatic assay confirmed protein presence according to iTRAQ findings and showed increased protein abundance levels and enzymatic activity in response to water-deficit. GO-term enrichment and analysis revealed terms involved in biotic and abiotic stress response, signaling, transport, cellular homeostasis and pentose metabolic processes, to be enriched in tef up-regulated proteins, while terms linked to ROS-producing processes under water-deficit, such as photosynthesis and associated light harvesting reactions, manganese transport and homeostasis, the synthesis of sugars and cell wall catabolism and modification, to be enriched in tef down-regulated proteins.

2017-11-21 | PXD007907 | Pride

Quantitative Proteomic Profiling of Cervicovaginal Fluid from Pregnant Women with Term and Preterm Birth

Project description:Preterm birth (PTB) is one of major causes of perinatal mortality and neonatal morbidity, but knowledge of its complex etiology is still limited. Here we present cervicovaginal fluid (CVF) protein profiles of pregnant women who subsequently delivered at spontaneous preterm or term, aiming to identify differentially expressed CVF proteins in PTB and term birth. The CVF proteome of women who sequentially delivered at preterm and term was analyzed using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with two-dimensional nanoflow liquid chromatography-tandem mass spectrometry (2D-nLC-MS/MS). We compared the CVF proteome of PTB (n=5) and control subjects (term birth, n=7) using pooled control CVF (term birth, n=20) as spike-in standard. We identified 1294 CVF proteins, of which 605 were newly identified proteins. Of 990 proteins quantified in both PTB and term birth, 52 proteins were significantly up/down-regulated in PTB compared to term birth. The differentially expressed proteins were functionally associated to immune response, endopeptidase inhibitors and structural constituent of cytoskeleton. Taken together, our study provide quantitative CVF proteome profiles of pregnant women who ultimately delivered at preterm and term. These promising results could help to improve the understanding of PTB etiology and to discover biomarkers for asymptomatic PTB.

2021-09-09 | PXD021401 | Pride

Synthetic yeast genome project

Project description:The experiment aimed to study the proteome variation in a yeast strain (YS031), which chromosome II was artificially synthezied, compared with the wild type strain (BY4741). Proteins were extracted from the yeast cells and digested with trypsin. The peptides were label with iTRAQ, separated with 2D LC (SCX and RP) and detected with a Q-Exactive MS. Proteome identification and quantification were performed with Mascot2.3 and iQuant3.0.

2018-10-27 | PXD003435 | Pride

Pig embryonic muscle iTRAQ analysis

Project description:Here, we performed the first iTRAQ-based proteomic analysis of early embryonic longissimus dorsi muscle from Landrance (LR) and miniature pig (Wuzhishan WZS) ranging from 21 to 42 days post coitus (dpc). 4431 proteins were identified. In both WZS and LR, the largest amount of differentially expressed proteins (DEPs) were found between 28 and 35 dpc. 252 breed-DEPs were selected by GO analysis, including 8 myofibrillar proteins. Only MYHCⅠ/IIA mRNA were detected due to early embryonic stages, and significantly higher expression of them were found in WZS during these 4 stages. MYHCⅠ was first found in WZS at 28 dpc and expressed in both breeds at later stages, while MYHCII protein was not detected until 35 dpc in both breeds. Thus, 33 myogenic breed-DEPs selected from last two stages were analyzed by STRING, which showed that some myofibrillar proteins (MYH1, TPM4, MYH10, et.al) and functional proteins (CSRP2, CASQ2, OTC, et.al), together with candidate myogenic proteins (H3F3A, HDGFRP2, et.al), probably participate in the regulatory network of myofiber formation. Thus, our study provides new data on myofiber type development during early embryo stages, which contributes to the improved understanding in the regulation mechanism of early myogenesis in agricultural animals.

2016-02-26 | PXD002481 | Pride

Proteomic analysis of eleven tissues of Chinese Giant Salamander (Andrias davidianus)

Project description:The Chinese giant salamander (CGS, Andrias davidianus) is the largest and longest-lived amphibian. Global and quantitative proteome analysis of multiple tissues would indicate tissue-specific mechanisms and investigate the function of each protein from a whole-organism perspective. Herein, this study performed proteome analysis of eleven tissues collected from adult female CGS using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with LC-MS/MS methods. Based on the predicted protein database from CGS transcriptome database previously obtained, we identified a total of 4607 proteins with quantitative information. Among them, 2153 proteins were shared by two iTRAQ 8-plex experiments with liver as common sample, and these proteins were used for subsequent analysis. Our data will be useful for future research into this large-genome species, as well as for vertebrate-wide comparative genomic, transcriptomic and proteomic studies.

2019-11-18 | PXD005648 | Pride

Comparative analysis of excretory–secretory products of muscle larvae of three isolates of Trichinella pseudospiralis by the iTRAQ method

Project description:we compared the differentially expressed proteins of excretory-secretory (ES) products in three isolates of T. pseudospiralis ML [muscle larvae from Russia (RUS), United States of America (USA) and Australia (AUS)] using isobaric tags for relative and absolute quantification (iTRAQ)-based technology.A total of 2,591 nonredundant proteins were identified, of which 65 (146), 72 (98) and 43 (103) significantly upregulated (downregulated) differentially expressed proteins were detected among pairwise comparisons (T4RUS vs T4USA, T4AUS vs T4USA and T4RUS vs T4AUS). In addition, GO annotation, KEGG and STRING analyses were carried out on the screened differentially altered proteins.

2020-05-07 | PXD017604 | 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