Browse
Submit Data
Databases
API
Help

Dataset Information

469 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The dataset to discover ESCC related proteins

ABSTRACT: To discover ESCC related proteins, we used SWATH to quantify the protein abundance between ESCC and adjacent tissues. Briefly, we pooled 10 ESCCtissues and their corresponding adjacent tissues for SWATH acquisition with three replicates.Three DDA repeats were also acquired with the pooled 10-paired ESCC tissue.The trypsin digested peptide mixture was analyzed by AB SCIEX 5600 (AB SCIEX).The database searching procedure was achieved using ProteinPilot v4.5 (AB Sciex). The database is IPI_homo_sapiens_V3.87.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Esophageal Epithelium

DISEASE(S): Esophagus Squamous Cell Carcinoma

SUBMITTER: Xue Hou

LAB HEAD: siqi liu

PROVIDER: PXD001764 | Pride | 2015-09-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DDA_01.group	Other
	DDA_01.wiff	Wiff
	DDA_01.wiff.scan	Wiff
	DDA_02.group	Other
	DDA_02.wiff	Wiff

Items per page:

1 - 5 of 22

Publications

Biomarker Discovery and Verification of Esophageal Squamous Cell Carcinoma Using Integration of SWATH/MRM.

Hou Guixue G Lou Xiaomin X Sun Yulin Y Xu Shaohang S Zi Jin J Wang Quanhui Q Zhou Baojin B Han Bo B Wu Lin L Zhao Xiaohang X Lin Liang L Liu Siqi S

Journal of proteome research 20150818 9

We propose an efficient integration of SWATH with MRM for biomarker discovery and verification when the corresponding ion library is well established. We strictly controlled the false positive rate associated with SWATH MS signals and carefully selected the target peptides coupled with SWATH and MRM. We collected 10 samples of esophageal squamous cell carcinoma (ESCC) tissues paired with tumors and adjacent regions and quantified 1758 unique proteins with FDR 1% at protein level using SWATH, in ...[more]

PMID: 26224564

Similar Datasets

Comprehensive proteomic analysis of Penicillium verrucosum

Project description:In the present study we used OTA producing Penicillium verrucosum to identify and quantify proteins of an organism with yet no protein information available. We were able to identify 3632 proteins in an "ab initio" translated database from DNA sequences of P. verrucosum. Additionally a SWATH analysis was done to find differentially regulated proteins at two different time points of the growth curve. We compared the proteins at the beginning and the end of the log phase.

2017-03-16 | PXD005459 | Pride

SWATH-MS dataset of Garcinia mangostana pericarp’s proteome across ripening stages

Project description:Data provided is derived from our research on comparing protein expression profiling of Garcinia mangostana (G. mangostana) Linn. on different ripening stages. Proteins were extracted from the pericarp of G. mangostana at three points of ripening stages (stage 0, 2 and 6) and digested with trypsin before being analyzed using 1 Dimensional and 2 Dimensional Information Dependent Acquisition Liquid Chromatography (1D and 2D IDA LC) coupled with sequential window acquisition of all theoretical fragment ion spectra (SWATH) analysis. This approach enable us to identify and relatively quantify protein in complex mixture. Protein identification was performed by matching tandem mass (MS/MS) spectra from 1D and 2D IDA to in-house-generated and UniProt databases using a database search algorithm software ProteinPilot (v4.2) (AB Sciex). Protein quantification was performed by analyzing protein peak areas extracted from SWATH analysis data sets using PeakView (v2.1) (AB Sciex) software. Finally, protein peaks were subjected to statistical analysis to compare relative protein peak areas between the sample groups.

2021-05-24 | PXD006295 | Pride

Metabolomics analysis of mouse gut microbiota

Project description:Liquid chromatography -mass spectrometry was performed on an AB Sciex TripleTOF 5600TM mass spectrometry system (AB SCIEX, USA) for nontargeted metabolomics analysis

2022-04-24 | PXD033405 |

Platform independent protein-based cell-of-origin subtyping of diffuse large B-cell lymphoma in formalin-fixed paraffin-embedded tissue

Project description:10 µm formalin-fixed paraffin-embedded tissue sections were deparaffinized with xylene; homogenization was performed in lysis-buffer (20 mM Tris-HCl, pH 8.8, 200 mM glycine, 200 mM DTT, 4% SDS)in an ultrasonic bath; samples were incubated under continuous agitation first at 99 °C for 30 min, then at 80 °C for 60 min, afterwards centrifuged at 12,000xg for 10 min. 50 µg of protein lysate were further processed according the GASP (Gel-assisted sample preparation) protocol; peptide identification (IDA, information dependent acquisition) and SWATH measurements by LC-MS/MS on TripleTOF5600 (AB Sciex)

2020-05-18 | PXD012317 | Pride

Zinc supply mediated by ZNT5-ZNT6 and ZNT7 is critical to glycosylphosphatidylinositol-anchored protein expression

Project description:Glycosylphosphatidylinositol (GPI)-anchored proteins play crucial roles in various enzyme activities, cell signaling and adhesion, and immune responses. ZNT type zinc transporter proteins mobilize cytosolic zinc to the extracellular space and intracellular compartments. Here, we report that the early secretory pathway ZNTs [ZNT5-ZNT6 heterodimers (ZNT5-6) and ZNT7 homodimers (ZNT7)], which supply zinc into the lumen of organelles, are essential for GPI-anchored protein expression on the cell surface. Loss of ZNT5-6 and ZNT7 zinc transport functions results in a significant reduction of GPI-anchored proteins similar to that of mutant cells lacking phosphatidylinositol glycan anchor biosynthesis (PIG) genes. Disrupted ZNT5 and ZNT7 genes in medaka fish show touch-insensitive phenotypes similar to those of zebrafish PIG mutants. These findings provide a previously unappreciated insight into the regulation of GPI-anchored protein expression and of protein quality control in the early secretory pathway.

2022-05-04 | PXD032172 | Pride

SWATH-MS based characterization for proteome profile data of chemicals

Project description:Profile data analysis is useful to reveal the mode of action of low molecular weight compounds. Although transcriptome data have been the main target of the profile data analysis, it is unknown whether omics data in different layers could deserve the profile data analysis. In the first place, what is not described as numerical data does not serve for analyses. Therefore, understanding the characteristics of omics data in different layers is crucial. In this study, we examined whether proteome data obtained by SWATH-MS (Sequential Window Acquisition of all Theoretical Mass Spectra) is useful to understand the mode of action of low molecular weight compounds. We demonstrated that proteome data obtained by SWATH-MS was useful for profile data analyses to the same extent as transcriptome data. Furthermore, we revealed a new mode of action of natural compound harmine as a result of profile data analysis using SWATH-MS data.

2023-02-22 | PXD032785 | Pride

APPLICATION OF A NOVEL PEPTIDE SPECTRAL LIBRARY USING SWATH ANALYSIS FOR THE QUANTITATION OF PROTEINS IN EX-DIAGNOSTIC CLINICAL SERUM SAMPLES FROM SHEEP

Project description:This project applies SWATH approach to analyse ex-diagnostic sheep serum samples from actual clinical cases submitted to The University of Queensland's School of Veterinary Science, Veterinary Laboratory Services (VLS) compared with serum of normal sheep.

2022-11-15 | PXD005077 | Pride

SWATH-based quantitative proteomics data derived from whole grain of Malaysian local pigmented and non-pigmented rice varieties

Project description:Information about protein expression in rice grain across both pigmented and non-pigmented rice varieties is still relatively scarce. The data provided here represent proteomic data obtained from selected 6 Malaysian local rice varieties with varying pigmentations (black, red and white). The selected pigmented rice varieties such as black (BALI and Pulut hitam 9) and red rice (MRQ100 and MRM16) have shown high antioxidant activities and non-pigmented rice (MRQ76 and MR297) contain amino acid and micronutrient contents. This project aimed to obtain global protein expression profile as well as differential protein expression between the selected pigmented and non-pigmented rice varieties particularly proteins with their functions responsible for nutritional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits. Integration of this proteomics dataset with other available in-house omics data could facilitate the identification of significant functional markers related to nutritional and quality traits. Total proteins were prepared from dehusked matured seeds harvested from three different rice plants of each variety (3 protein samples per variety). The proteins were trypsin digested before subjected to SWATH-MS proteomics analysis. Proteins were identified by matching tandem mass (MS/MS) spectra from both 1D and 2D IDA to Oryza sativa japonica and indica rice databases available at UniProt by using ProteinPilot software (v4.2) (AB Sciex). Quantification of proteins was carried out by determining protein peak areas extracted from SWATH analysis data sets using PeakView (v2.1) (AB Sciex) software. Differentially expressed protein between varieties were identified using T-test analysis with a set threshold for fold change ± 1.5 and p‐value < 0.05.

2020-04-27 | PXD018338 | Pride

Cytosol - Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism

Project description:Enriched Arabidopsis cytosol (cell culture) fractionated by SCX (15 fractions) and analysed by Q-TOF nanoLC-MS/MS (AB Sciex QStar Elite)

2011-03-01 | PRD000391 | Pride

SWATH-MS Analysis of Striatal Synaptic Mitochondria from Pink1 KO rats

Project description:This study investigates the proteomic alterations in striatal synaptic mitochondria isolated from 3-month-old wild-type and Pink1 KO rats using the SWATH-MS strategy. This dataset consists of 32 raw MS files, comprising 8 DIA (SWATH) and 24 DDA runs on a TripleTOF 5600 (SCIEX). Our findings revealed synaptic mitochondrial proteomic changes due to loss of Pink1.

2016-09-28 | PXD004558 | Pride