PXD035055

PXD035055 is an original dataset announced via ProteomeXchange.

Title	DirectMS1 analysis of cell response of A2780 to topotecan
Description	Omics technologies focus on uncovering the complex nature of molecular mechanisms in cells and organisms, including biomarkers and drug targets discovery. Aiming at these tasks, we see that information extracted from omics data is still underused. In particular, characteristics of differentially regulated molecules can be combined in a single score to quantify the signaling pathway activity. Such a metric can be useful for comprehensive data interpretation to follow: 1) developing molecular responses in time; 2) potency of a drug on a certain cell culture; 3) ranking the signaling pathway activity in stimulated cells; and 4) integration of the omics data and assay-based measurements of cell viability, cytotoxicity and proliferation. With recent advances in ultrafast mass spectrometry for quantitative proteomics allowing data collection in a few minutes, proteomics score for cellular response to stimuli can become a fast, accurate and informative complement to bioassays. Here we utilized an interquartile-based selection of differentially regulated features and a variety of schemes for quantifying cellular responses to come up with the quantitative metric for total cellular response and pathway activity. Validation was performed using antiproliferative and virus assays and label-free proteomics data collected for cancer cells subjected for drug stimulation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:32:46.296.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lev Levitsky
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-03 00:25:45	ID requested
1	2024-03-11 04:17:18	announced
⏵ 2	2024-10-22 06:32:46	announced	2024-10-22: Updated project metadata.

10.1002/PMIC.202200275;

submitter keyword: DirectMS1, LC-MS, A2780, topotecan, cell line

Irina A. Tarasova
contact affiliation	INEPCP FRCCP RAS, Moscow, Russia
contact email	iatarasova@yandex.ru
lab head
Lev Levitsky
contact affiliation	INEPCP RAS
contact email	lev.levitsky@phystech.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/03/PXD035055

PRIDE project URI

• PRIDE
  1. PXD035055
     1. Label: PRIDE project
     2. Name: DirectMS1 analysis of cell response of A2780 to topotecan