Proteomics

Dataset Information

351

Comparison of Lung Cancer Proteome Profiles 4: DDA


ABSTRACT: The goal of this project is to compare label free quantification, chemical labeling with tandem mass tags, and data independent acquisition discovery proteomics approaches using lung squamous cell carcinomas and adjacent lung tissues. This additional single sample LC-MS/MS analysis with data dependent acquisition was performed to enable direct comparison to the PRIDE dataset, titled, "Comparison of Lung Cancer Proteome Profiles 3: DIA," where single samples were analyzed with LC-MS/MS using data independent acquisition.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo sapiens  

TISSUE(S): Lung

DISEASE(S): Lung Cancer

SUBMITTER: John Koomen  

LAB HEAD: John Koomen, PhD

PROVIDER: PXD005733 | Pride | 2017-02-16

REPOSITORIES: Pride

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Publications

Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms.

Stewart Paul A PA   Fang Bin B   Slebos Robbert J C RJ   Zhang Guolin G   Borne Adam L AL   Fellows Katherine K   Teer Jamie K JK   Chen Y Ann YA   Welsh Eric E   Eschrich Steven A SA   Haura Eric B EB   Koomen John M JM  

Proteomics 20170301 6


Discovery proteomics experiments include many options for sample preparation and MS data acquisition, which are capable of creating datasets for quantifying thousands of proteins. To define a strategy that would produce a dataset with sufficient content while optimizing required resources, we compared (1) single-sample LC-MS/MS with data-dependent acquisition to single-sample LC-MS/MS with data-independent acquisition and (2) peptide fractionation with label-free (LF) quantification to peptide f  ...[more]

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