Evidence map›Paper›PMID 39962197›Full record

ReviewNature protocols2025

Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues.

Qing Kay Li, T Mamie Lih, David J Clark, Lijun Chen, Michael Schnaubelt, Hui Zhang

Abstract readReview
In one paragraph

Review in Nature protocols, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Review
  5. Review
  6. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Qing Kay Li *Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA. qli23@jhmi.edu.
T Mamie Lih *Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
David J ClarkDepartment of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
Lijun ChenDepartment of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
Michael SchnaubeltDepartment of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
Hui ZhangDepartment of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA. huizhang@jhu.edu.ORCID 0000-0001-8726-7098

Funding

Proteogenomic Characterization of Tumor Tissues and Preclinical Models with High PrecisionU24CA271079 · NCI · JOHNS HOPKINS UNIVERSITY · PI DANIEL Wanyui CHAN, Hui Zhang · 2022 to 2026
$6.6M
NCI NIH HHS U24 CA271079U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) U24CA271079
6 · The paper itself

Abstract

Deep-scale, mass spectrometry-based proteomic studies by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program involves tissue lysis using urea buffer before data acquisition via mass spectrometry for quantitative global proteomic and phosphoproteomic analysis. This is described in a 2018 protocol

Indexed as

DNA-Binding ProteinsMembrane ProteinsNeoplasmsProteomicsSonicationAnimalsHumansMiceTandem Mass SpectrometryDNA-Binding ProteinsMembrane Proteins

Identifiers

PMID39962197
PMCPMC12286572

What OpenQuestion holds

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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 OpenQuestion graph.