PXD014847

PXD014847 is an original dataset announced via ProteomeXchange.

Title	Isoform-resolved Correlation Analysis Between mRNA Abundance Dynamics and Protein Level Degradation
Description	We employed an optimized, sensitive DIA-MS method on a high-resolution Orbitrap platform and re-measured the proteomic samples used in a previous study, in which the heterogeneity of HeLa cells across different research labs was analyzed by a multi-omic approach. Using the same MS sample sets of all HeLa strains we achieved higher sensitivity compared to our previous SWATH-MS results that were acquired on a TripleTOF instrument (5600 model). To benefit from the significantly improved sensitivity of this single-shot DIA-MS for both proteomic and protein turnover analysis, we analyzed the samples originating from six HeLa Kyoto strains and six HeLa CCL2 strains to profile both total protein-level abundances and the proxy protein turnover rates (Kloss, by pulsed SILAC labeling) across cell lines. Our results emphasized the importance of relative mRNA-protein turnover rate correlation analysis. The dataset demonstrate that specific biological processes, cellular organelles, subunits of organelles, and individual protein isoforms may have distinctive degradation rate and the corresponding buffering or concerting protein turnover control across cancer cell lines.
HostingRepository	PRIDE
AnnounceDate	2020-03-11
AnnouncementXML	Submission_2020-03-24_05:07:57.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Barbora Salovska
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-31 01:24:36	ID requested
1	2020-03-11 06:53:13	announced
⏵ 2	2020-03-24 05:07:59	announced	2020-03-24: Updated publication reference for PubMed record(s): 32175694.

Salovska B, Zhu H, Gandhi T, Frank M, Li W, Rosenberger G, Wu C, Germain PL, Zhou H, Hodny Z, Reiter L, Liu Y, Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation. Mol Syst Biol, 16(3):e9170(2020) [pubmed]

submitter keyword: DIA mass spectrometry, Protein turnover, Pulsed SILAC, Alternative splicing, Protein isoform, Correlation analysis

Yansheng Liu
contact affiliation	Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
contact email	yansheng.liu@yale.edu
lab head
Barbora Salovska
contact affiliation	Institute of Molecular Genetics of the Czech Academy of Sciences
contact email	salovska@img.cas.cz
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/2020/03/PXD014847

PRIDE project URI

• PRIDE
  1. PXD014847
     1. Label: PRIDE project
     2. Name: Isoform-resolved Correlation Analysis Between mRNA Abundance Dynamics and Protein Level Degradation