Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DDA files of human cancer cells for the NCI-60 SWATH project PXD003539

ABSTRACT: This is the raw files for the DDA library used for intepreting the NCI-60 SWATH project PXD003539

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Cell Line Cell

DISEASE(S): Lung Cancer,Colon Cancer,Acute Leukemia,Prostate Cancer,Brain Cancer,Kidney Cancer,Malignant Neoplasm Of Ovary,Breast Cancer

SUBMITTER: Tiannan Guo

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD009597 | Pride | 2019-10-21

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.

Guo Tiannan T Luna Augustin A Rajapakse Vinodh N VN Koh Ching Chiek CC Wu Zhicheng Z Liu Wei W Sun Yaoting Y Gao Huanhuan H Menden Michael P MP Xu Chao C Calzone Laurence L Martignetti Loredana L Auwerx Chiara C Buljan Marija M Banaei-Esfahani Amir A Ori Alessandro A Iskar Murat M Gillet Ludovic L Bi Ran R Zhang Jiangnan J Zhang Huanhuan H Yu Chenhuan C Zhong Qing Q Varma Sudhir S Schmitt Uwe U Qiu Peng P Zhang Qiushi Q Zhu Yi Y Wild Peter J PJ Garnett Mathew J MJ Bork Peer P Beck Martin M Liu Kexin K Saez-Rodriguez Julio J Elloumi Fathi F Reinhold William C WC Sander Chris C Pommier Yves Y Aebersold Ruedi R

iScience 20191031

Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure cycling technology and SWATH mass spectrometry. We developed the DIA-expert software to curate and visualize the SWATH data, leading to reproducible detection of over 3,100 SwissProt proteotypic proteins and systematic quantification of pathway activities. Stoichiometric relationships of interacting proteins for DNA replication, repair, the chromatin remodeling NuRD complex, β-catenin, RNA metabolism, and ...[more]

PMID: 31733513

Similar Datasets

Dynamic of the Grb2 interactome in primary cells by DDA-MS

Project description:We applied AP-MS to quantify Grb2 interaction dynamics in primary T cells. Data generated here in shotgun/DDA mode were used to build a high quality Grb2 binders-specific SWATH assay library for high-throughput targeted analysis of DIA data.

2017-03-09 | PXD003973 | Pride

Enterococcus faecalis V583, Part 1

Project description:Genome-scale models represent the link between an organism's genetic information and experimentally observable biological phenotypes. They facilitate metabolic engineering and the discovery of network properties such as the identification of novel drug targets. Most commonly, metabolite consumption data is used to limit the solution space, sometimes in combination with gene expression data. However, information about gene expression only poorly correlates with the abundance of the respective proteins within the cell. As such, we developed a method to map and integrate the whole-cell proteome into genome-scale models on the example of lactic acid bacteria (LAB). To the best of our knowledge, this work represents the first effort to integrate proteome data into genome-scale models on such a scale.

2016-12-06 | PXD001576 | Pride

A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics

Project description:Comprehensive spectral libraries are essential in sequential window acquisition of all theoretical mass spectra (SWATH-MS) based high throughput proteomic studies. Even though SWATH-MS assays provide robust quantitative proteomics data its applications to human T-cell studies are limited by the lack of a human T-cell spectral library. To address this resource gap, we generated a high-quality spectral library containing data for 3,941 unique proteins from primary human T-cells across genetically unrelated donors. SWATH-MS analysis of 18 primary T-cell samples using the new human T-cell spectral library identified and quantified 3,022 proteins at 1% FDR, whereas the larger Pan-human spectral library identified and quantified 2,794 proteins, with only 34% overlap. Combining the two libraries resulted in 4,061 proteins, covering ~50% of proteins in immune-related pathways. Overall, this data suggests DDA-MS is suited to discovery projects through to its enhanced sensitivity and SWATH-MS is suited to high-throughput projects.

2020-10-19 | PXD019446 | Pride

Enterococcus faecalis V583 - data analysis

2016-12-06 | PXD002869 | Pride

∆glnA Enterococcus faecalis V583 - data analysis

Project description:A group of gram positive bacteria that share the characteristic of fermenting hexose sugars to lactic acid are generally referred to as lactic acid bacteria (LAB). Enterococcus faecalis is one of the widely studied LABs due to a multiutude of reasons. On the one hand, it plays an important role in dairy industry, being for example a starter in cheese cultures. On the other hand, it accounts for a large part of the infections caused by the LABs in hospital environments. During the past few years, it developed resistance against most of the major antibiotics. Here, in an attempt to study its adaptive metabolism, a glutamine synthetase mutant (∆glnA) of E. faecalis was subjected to pH shift and the results from the integrative analysis of its metabolic network were compared to those of the wild type. The proteome data generated in this study were used to constrain the genome-scale metabolic network at two pH level, aiming to reduce the solution space and improve the accuracy of model simulation. This data particularly helped to come up with a new design for the amino acid transport system in the genome-scale model, resulting in an accurate reproduction of the metabolic behaviour of E. faecalis.

2022-01-14 | PXD030778 | Pride

Yeast proteomic analysis upon temperature shift

Project description:DIA/SWATH analysis of yeast upon temperature shift.

2021-06-28 | PXD016320 | Pride

Comprehensive spectral library generation for identification and quantification of endometrial cancer protein biomarkers in cervico-vaginal fluid

Project description:This study focuses on the potential of detecting endometrial cancer based on the proteins and peptides expressed in cervico-vaginal fluid.Sequential window acquisition of all theoretical mass spectra (SWATH-MS), an accurate and reproducible platform for analysing biological samples, offers a technological advance for biomarker discovery due to its reproducibility, sensitivity and potential for data re-interrogation. SWATH-MS requires a spectral library in order to identify and quantify peptides from multiplexed mass spectrometry data.Here, we present a spectral library of thousands of proteins in the cervico-vaginal fluid of women with or at risk of endometrial cancer. Pooled cervico-vaginal fluid samples from 19 women, comprising of 9 endometial cancer cases(both endometriod and non-endometriod), 3 atypical hyperplasias and 7 controls (symptomatic post-menopausal women with no evidence of endometrial cancer) were used for library generation. We have combined these data with a library of over 6,000 proteins generated based on mass spectrometric analysis of two endometrial cancer cell lines This important resource will enable the identification of endometrial cancer biomarkers in cervico-vaginal fluid and advances our knowledge of the role of proteomics in endometrial cancer detection.

2021-08-13 | PXD025925 | Pride

The DIALib-QC software tool for the systematic assessment of spectral library quality in data-independent acquisition proteomics

Project description:DIALib-QC (DIA library quality control) tool is used for the systematic evaluation of a spectral library’s characteristics, completeness and mass-accuracy ensuring correct identification and accurate quantitation of peptides and proteins from DIA/SWATH processing tools.

2020-10-16 | PXD020953 | Pride

A tissue-based draft map of the murine MHC class I immunopeptidome

Project description:The array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC class I immunopeptidome. Although the MHC class I immunopeptidome is ubiquitous in mammals and represents a critical component of the adaptive immune system, very little is known about its baseline composition across all tissues and organs in vivo. In this study, we applied mass spectrometry (MS) technologies to draft a tissue-based atlas of the MHC class I immunopeptidome in the C56BL/6 mouse model. Overall, 19 normal mouse tissues were extracted and a total number of ~30,000 high-confidence H2Db/Kb-associated peptides were identified and annotated in the atlas. The raw MS output files, the catalogue of H2Db/Kb-associated peptides, the tissue origin(s) of individual peptides and the H2Db/Kb-specific peptide spectral libraries, which consist of consensus spectra calculated from repeat measurements of the same peptide sequence, were shared via the SysteMHC Atlas project (dataset identifier SYSMHC00018). We expect that this unique dataset will be further expended in the future and will be re-used by the community to 1) investigate the tissue-specificity of the immunopeptidome, 2) perform highly reproducible spectral library-based analysis of immunopeptidomes from mice cohorts, and 3) rapidly identify disease-specific H2Db/Kb peptide antigens from various mouse models of autoimmune diseases and cancers.

2018-06-19 | PXD008733 | Pride

Yeast Nat Nt-acetylation SWATH MS

Project description:Yeast strains (wild type, Naa10 KO and Naa20 KO, resp: wt, natA-delta and natB-delta) were profiled for full proteome analysis by SWATH MS

2020-12-15 | PXD015217 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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