Evidence map›Paper›PMID 42763858›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2027

Mass Spectrometry-Based Proteomics of Intestinal Organoids.

Roei Cohen-Almagor, Samna Sagadevan, Paloma Ordóñez-Morán

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2027. 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

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

3 authors.

Roei Cohen-AlmagorTranslational Medical Sciences Unit, School of Medicine, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK.
Samna SagadevanTranslational Medical Sciences Unit, School of Medicine, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK.
Paloma Ordóñez-MoránTranslational Medical Sciences Unit, School of Medicine, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, UK. paloma.ordonezmoran@nottnigham.ac.uk.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Proteomics, the large-scale study of proteins, enables the identification, quantification, and functional characterization of proteins, revealing post-translational modifications and protein interactions that are not apparent from transcriptomic data. Human organoids, which recapitulate the structural and functional complexity of native epithelial tissues, provide powerful tools to study disease mechanisms and personalize therapies. However, their culture poses challenges for efficient protein extraction and reproducible analysis. Here, we present a proteomics workflow optimized to maximize protein recovery from Matrigel-encased organoids. Samples were processed using S-Trap microcolumns to minimize losses, followed by liquid chromatography-mass spectrometry (LC-MS) in data-independent acquisition (DIA/SWATH-MS) mode for comprehensive, untargeted quantification. Library-free computational analysis using DIA-NN, combined with differential expression analysis, enabled sensitive detection of key proteins in intestinal organoids.

Indexed as

Intestinal MucosaIntestinesLiquid Chromatography-Mass SpectrometryMass SpectrometryOrganoidsProteomeProteomicsHumansProteomeAmicaDIA-NNIntestinal organoidsLiquid chromatography–mass spectrometryProtein quantificationProteomics

Identifiers

PMID42763858

What OpenQuestion holds

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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.