PXD057632-1

PXD057632 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-07 10:49:48	ID requested
⏵ 1	2025-05-14 14:56:12	announced

Dataset with its publication pending

submitter keyword: Aneuploidy, Quantitative proteomics, Protein turnover, DIA, Drug resistance,Multiplex-DIA, pulse SILAC

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

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PRIDE project URI

• PRIDE
  1. PXD057632
     1. Label: PRIDE project
     2. Name: A Robust Multiplex-DIA Workflow Profiles Protein Turnover Regulations Associated with Cisplatin Resistance and Aneuploidy