Evidence map›Paper›PMID 39554001›Full record

ArticlebioRxiv : the preprint server for biology2024

A Comprehensive and Robust Multiplex-DIA Workflow Profiles Protein Turnover Regulations Associated with Cisplatin Resistance.

Barbora Salovska, Wenxue Li, Oliver M Bernhardt, Pierre-Luc Germain, Tejas Gandhi, Lukas Reiter, Yansheng Liu

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Barbora SalovskaDepartment of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
Wenxue LiDepartment of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
Oliver M BernhardtBiognosys Zurich-Schlieren, Switzerland.
Pierre-Luc GermainInstitute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
Tejas GandhiBiognosys Zurich-Schlieren, Switzerland.
Lukas ReiterBiognosys Zurich-Schlieren, Switzerland.
Yansheng LiuDepartment of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.

Funding

Understanding proteome remodeling in aneuploidyR01GM137031 · NIGMS · YALE UNIVERSITY · PI LIU, YANSHENG · 2020 to 2024
$2.0M
NIGMS NIH HHS R01 GM137031
6 · The paper itself

Abstract

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 and robust workflow that integrates a novel machine learning strategy and channel-specific statistical filtering, enabling dynamic adaptation to systematic or temporal variations in channel ratios. This allows comprehensive profiling of protein turnover throughout the pSILAC experiment without relying solely on the highest channel signals. Additionally, we developed

Indexed as

AneuploidyDIADrug resistanceMass spectrometryMultiplex DIAProtein turnoverpulse SILAC

Identifiers

PMID39554001
PMCPMC11565775

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.