PXD057632 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | A Robust Multiplex-DIA Workflow Profiles Protein Turnover Regulations Associated with Cisplatin Resistance and Aneuploidy |
Description | Measuring protein turnover is essential for understanding cellular biological processes and advancing drug discovery. The multiplex-DIA mass spectrometry (DIA-MS) approach, combined with dynamic SILAC labeling (pulse-SILAC, or pSILAC), has proven to be a reliable method for analyzing protein turnover and degradation kinetics. Previous multiplex-DIA-MS workflows have employed various strategies, including leveraging the highest isotopic labeling channels of peptides to enhance the detection of isotopic MS signal pairs or clusters. In this study, we introduce an improved workflow that integrates a novel machine learning strategy and channel-specific statistical filtering, enabling dynamic adaptation to systematic variations in channel ratios throughout pSILAC and SILAC experiments. These functions were evaluated to significantly improve both the comprehensiveness and accuracy of protein turnover profiling. In addition, we developed Our integrative workflow was benchmarked on both 2-channel and 3-channel standard DIA datasets and across two mass spectrometry platforms, demonstrating its broad applicability. Applying this workflow to an aneuploid cancer cell model before and after developing cisplatin resistance, we discovered a remarkable negative correlation between transcript regulation and protein degradation for major protein complex subunits elucidating the proteome buffering mechanism in genome aneuploidy. |
HostingRepository | PRIDE |
AnnounceDate | 2025-05-14 |
AnnouncementXML | Submission_2025-05-14_14:56:12.254.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; timsTOF Ultra |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-11-07 10:49:48 | ID requested | |
⏵ 1 | 2025-05-14 14:56:12 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Aneuploidy, Quantitative proteomics, Protein turnover, DIA, Drug resistance,Multiplex-DIA, pulse SILAC |
Contact List
Yansheng Liu |
contact affiliation | Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA |
contact email | yansheng.liu@yale.edu |
lab head | |
Barbora Salovska |
contact affiliation | Yale Cancer Biology Institute |
contact email | salovska.b@gmail.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD057632
- Label: PRIDE project
- Name: A Robust Multiplex-DIA Workflow Profiles Protein Turnover Regulations Associated with Cisplatin Resistance and Aneuploidy