Evidence map›Paper›PMID 32534439›Full record

ArticleiScience2020

Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes.

Stefani N Thomas, Betty Friedrich, Michael Schnaubelt, Daniel W Chan, Hui Zhang, Ruedi Aebersold

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in iScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing 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

17 citing papers in PubMed.

  1. Article
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  5. Article
  6. Quantitative Aspects of the Human Cell Proteome.International journal of molecular sciences · 2023
    Review
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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.

Stefani N ThomasDepartment of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
Betty FriedrichDepartment of Biology, Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
Michael SchnaubeltDepartment of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
Daniel W ChanDepartment of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
Hui ZhangDepartment of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Electronic address: huizhang@jhu.edu.
Ruedi AebersoldDepartment of Biology, Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; Faculty of Science, University of Zürich, Zürich, Switzerland. Electronic address: aebersold@imsb.biol.ethz.ch.

Funding

Proteome Characterization Center: A Genoproteomics Pipeline for Cance ResearchU24CA160036 · NCI · JOHNS HOPKINS UNIVERSITY · PI CHAN, DANIEL WANYUI, ZHANG, HUI · 2011 to 2016
$10.7M
Glycoprotein biomarkers for the early detection of aggressive prostate cancerU01CA152813 · NCI · JOHNS HOPKINS UNIVERSITY · PI ZHANG, HUI · 2010 to 2021
$6.2M
The Comprehensive Proteome Characterization Center at Johns Hopkins: High Precision Discovery and Confirmation of Genoproteomic TargetsU24CA210985 · NCI · JOHNS HOPKINS UNIVERSITY · PI CHAN, DANIEL WANYUI, ZHANG, HUI · 2016 to 2020
$5.3M
NCI NIH HHS U01 CA152813NCI NIH HHS U24 CA160036NCI NIH HHS U24 CA210985
6 · The paper itself

Abstract

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) established a harmonized method for large-scale clinical proteomic studies. SWATH-MS, an instance of data-independent acquisition (DIA) proteomic methods, is an alternate proteomic approach. In this study, we used SWATH-MS to analyze remnant peptides from the original retrospective TCGA samples generated for the CPTAC ovarian cancer proteogenomic study. The SWATH-MS results recapitulated the confident identification of differentially expressed proteins in enriched pathways associated with the robust Mesenchymal high-grade serous ovarian cancer subtype and the homologous recombination deficient tumors. Hence, SWATH/DIA-MS presents a promising complementary or orthogonal alternative to the CPTAC proteomic workflow, with the advantages of simpler and faster workflows and lower sample consumption, albeit with shallower proteome coverage. In summary, both analytical methods are suitable to characterize clinical samples, providing proteomic workflow alternatives for cancer researchers depending on the context-specific goals of the studies.

Indexed as

Biological SciencesCancer Systems BiologyProteomics

Identifiers

PMID32534439
PMCPMC7298555

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Registered trials

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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.