MassIVE MSV000084903

Complete Public PXD017388

Reproducible label-free quantitative proteomics profiling cellular responses to engineered nanomaterials

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Description

Proteomic data from engineered nanomaterial- treated THP-1 cells. Time points at 12 hours; 4 biological replicates for each treatment. Human THP-1 cells were either mock-treated (control) or treated with engineered nanomaterials (ENMs). Four biological replicates were used for each sample group (Control, or ENM treatment at either the low or high dosage). In the block design scheme for LC-MS analysis, samples treated with two different ENMs were assign into an analytical block (2 ENM X 2 dosages/ENM X 4 replicates = 16 samples). Four control samples were also included in each block, yielding 20 samples per block. Blocks of samples were divided into two processing batches. Samples in each batch were processed simultaneously from cell culture, to treatment with ENMs, and finally to proteomic sample preparation for LC-MS analysis (including trypsin digestion). [doi:10.25345/C5C67N] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: proteomics ; label-free quantification ; large cohort

Contact

Principal Investigators:
(in alphabetical order) 		Wei-Jun Qian, Pacific Northwest National Laboratory, United States
Submitting User: alchemistmatt

Publications

Tong Zhang, Matthew J. Gaffrey, Dennis G. Thomas, Thomas J. Weber, Becky M. Hess, Karl K.Weitz, Paul D. Piehowski, Vladislav A. Petyuk, Ronald J. Moore, Wei-Jun Qian, and Brian D. Thrall.
A proteome-wide assessment of the oxidative stress paradigm for metal and metal-oxide nanomaterials in human macrophages.
NanoImpact. 2020 Jan; 17: 100194. doi: 10.1016/j.impact.2019.100194.

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Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
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