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Dataset Information
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Dataset Name:
Proteomic cellular signatures of kinase inhibitor-induced cardiotoxicity

Dataset Description:
Drug Toxicity Signature Generation Center (DToxS) at the Icahn School of Medicine at Mount Sinai is an integral part of the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. A key aim of DToxS is to generate both proteomic and transcriptomic signatures that cab predict adverse effects, especially cardiotoxicity, of drugs approved by the Food and Drug Administration. Towards this goal, high throughput shot-gun proteomics experiments (317 cell line/drug combinations + 64 HeLa control lysates) have been conducted at the Center for Advanced Proteomics Research at Rutgers-New Jersey Medical School. The integrated proteomic and transcriptomic signatures have been used for computational network analysis to identify cellular signatures of cardiotoxicity that may predict drug-induced toxicity and possible mitigation of such toxicities by mixing different drugs. Both raw and processed proteomics data have been carefully controlled for quality and have been made publicly available via the PRoteomics IDEntifications (PRIDE) database. As such, this broad drug-stimulated proteomic dataset is valuable for the prediction drug toxicities and their mitigation.

--Data Files in Package:
Enriched Proteomic Pathways (Level 5).tsv

--Metadata Files In Package:
Antibody_Metadata.txt
DatasetMetadata.txt
Primary_Cell_Metadata.txt
ProteomicsExperimentalMetadata.txt
Small_Molecule_Metadata.txt

--Processing Pipeline Specifications In Package:
ProcessingPipelineSpecifications.txt

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Center-specific Information
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Center Name:
DToxS

LINCS Dataset ID:
LDS-1579

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Assay Information
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Assay Overview:
High throughput shot-gun proteomics experiments have been conducted for 317 cell line/drug combinations (from four primary human cardiomyocyte cell lines purchased from PromoCell) and 64 HeLa control lysates. The proteins contained in cell samples were isolated and digested into peptides, following by the LC-MS/MS assay of resulted peptide compositions. The RAW data files generated from the MS assay were analyzed by MaxQuant software to map detected peptides to corresponding proteins.

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Date Updated:

Date Retrieved from Center:
2020-2-21

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Metadata Information
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Metadata information regarding the entities used in the experiments is included in the accompanied metadata. A metadata file per entity category is included in the package. For example, the metadata for all the cell lines that were used in the dataset are included in the Cell_Lines_Metadata.txt file.
Descriptions for each metadata field can be found here: http://www.lincsproject.org/data/data-standards/
