PXD022992

PXD022992 is an original dataset announced via ProteomeXchange.

Title	Data-independent Acquisition-based Proteome and Phosphoproteome Profiling across Six Melanoma Cell Lines
Description	The rapid documentation of the steady-state gene expression landscape of the cells used in particular experiments may help to improve the reproducibility of scientific research. Here we applied a data-independent acquisition mass spectrometry (DIA-MS) method, coupled with a peptide spectral-library free data analysis workflow, to measure both proteome and phosphoproteome of a melanoma cell line panel with different metastatic properties. For each cell line, the single-shot DIA-MS detected 8,100 proteins and almost 40,000 phosphopeptides in the respective measurement of two hours. Benchmarking the DIA-MS data towards the RNA-seq data and tandem mass tag (TMT)-MS results from the same set of cell lines demonstrated comparable qualitative coverage and quantitative reproducibility. Our data confirmed the high but complex mRNA~protein and protein~phospsite correlations. The results successfully established DIA-MS as a strong and competitive proteotyping approach for cell lines.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:20:02.790.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yansheng Liu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-08 02:25:15	ID requested
1	2021-03-14 23:25:45	announced
⏵ 2	2024-10-22 05:20:03	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Melanoma, Proteome, Cell lines,DIA, Metastasis, Phosphoproteome

Yansheng Liu
contact affiliation	Yale University School of Medicine
contact email	yansheng.liu@yale.edu
lab head
Yansheng Liu
contact affiliation	Yale University School of Medicine
contact email	yansheng.liu@yale.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/2021/03/PXD022992

PRIDE project URI

• PRIDE
  1. PXD022992
     1. Label: PRIDE project
     2. Name: Data-independent Acquisition-based Proteome and Phosphoproteome Profiling across Six Melanoma Cell Lines