Dataset Information

Phospho-proteomics analysis of ATR inhibitor responses in sensitive and resistant human breast cancer cells

ABSTRACT: To search in an unbiased manner for the specific mechanisms causing differential ATRi sensitivity, we performed total and phosphoproteomic analyses using tandem mass tagging (TMT) mass spectrometry. Extracted proteins were compared between three sensitive and three resistant human breast cancer cell lines, treated with DMSO, ATR inhibitor 1h or 24h, using quantitative proteomics.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Breast Cancer

SUBMITTER: Faraz Mardakheh

LAB HEAD: Sarah McClelland

PROVIDER: PXD061444 | Pride | 2026-05-19

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	20230421_AudreyLumeau_TMT_fraction1.raw	Raw
	20230421_AudreyLumeau_TMT_fraction2.raw	Raw
	20230421_AudreyLumeau_TMT_fraction3.raw	Raw
	20230421_AudreyLumeau_TMT_fraction4.raw	Raw
	20230421_AudreyLumeau_TMT_fraction5.raw	Raw

Items per page:

1 - 5 of 13

Similar Datasets

Project description:Bile has gained increasing attention for its potential to reflect the overall health of the biliary system. Proteomic analysis of bile could deepen our understanding of the molecular pathophysiology of biliary disease and injury and provides a potential source of diagnostic biomarkers. With the emergence of normothermic machine perfusion (NMP) prior to liver transplantation, bile samples can be easily collected and analyzed. However, the unique composition of bile, including high concentrations of endogenous detergents and salts, can make application of proteomics challenging. In this study, we systematically evaluated a variety of available trypsin-digestion methods to optimize proteomics analysis of bile obtained from human NMP livers. Bile was collected from 12 human donor livers that were accepted for transplantation after NMP viability assessment. We performed tryptic digestion using 6 different methods: in-gel, in-solution, S-Trap, SMART, EasyPep, and filter-aided sample purification, with or without an additional precipitation step prior to digestion. Untargeted, data-independent acquisition proteomics was performed using an Exploris 480 mass spectrometer coupled with a FAIMS device. The methods were judged for total protein IDs, variation, and specific protein characteristics to determine the most optimal method. A total of 4650 unique proteins were identified across all samples and all methods. Methods involving precipitation identified substantially more proteins (4500 vs 3815, respectively). In-gel crude was the exception, identifying a comparable number of proteins to precipitated in-gel digest. We found minimal differences in the mass, cellular component, or hydrophobicity of identified proteins between methods. Intra-method variability was notably diverse, with in-gel, in-solution, and EasyPep outperforming other methods with considerably less variation. Age-related biological comparisons revealed significant disparities in protein abundances between methods, but younger donors consistently showed upregulation of metabolic-related processes compared to older donors. Older donors showed upregulation of immune response and cell cycle-related processes. The digestion method used for proteomic analysis of bile can heavily influence the results obtained. A method of protein purification appears to be essential for sufficient quality mass spectrometry runs and subsequent data. Sample processing speed, cost, cleanliness, and reproducibility should be carefully considered when selecting a protein digestion method for this difficult sample type.

Dataset Information

Phospho-proteomics analysis of ATR inhibitor responses in sensitive and resistant human breast cancer cells

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets