Evidence map›Paper›PMID 41018846›Full record

ArticleBiology methods & protocols2025

A robust protocol for proteomic profiling of secreted proteins in conditioned culture medium.

Takayoshi Otsuka, Atsushi Hatano, Masaki Matsumoto, Hideaki Matsui

Abstract read
In one paragraph

Article in Biology methods & protocols, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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

4 authors.

Takayoshi OtsukaDepartment of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata 951-8585, Japan.ORCID https://orcid.org/0000-0002-7954-0637
Atsushi HatanoDepartment of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan.
Masaki MatsumotoDepartment of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan.
Hideaki MatsuiDepartment of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata 951-8585, Japan.ORCID https://orcid.org/0000-0003-4908-1035

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Reliable secretome analysis is crucial for understanding cellular communication and developing therapeutic strategies. However, conventional protein quantification methods, such as the bicinchoninic acid (BCA) assay, can overestimate protein concentrations in concentrated culture media, leading to inconsistent protein loading and compromised quantitative accuracy in mass spectrometry-based proteomics. To address this methodological challenge, we developed an improved sample preparation method for secretome analysis. Our approach introduces a concentration rate-based normalization method that adjusts sample volumes according to the ultrafiltration concentration ratio, ensuring more consistent protein loading across samples. This method enabled reliable identification of 3468 secreted proteins with high reproducibility (

Indexed as

conditioned mediumDIA proteomicssecreted proteinssilver stain

Identifiers

PMID41018846
PMCPMC12461699

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.