Evidence map›Paper›PMID 41552556›Full record

ArticleACS omega2026

Rapid and Label-Free Structural Proteomics Using One-Step Swift Trypsin LiP-MS.

Yasuomi Miyashita, Ryo Konno, Satoshi Ogasawara, Yusei Okuda, Yuuki Takamuku, Toshio Moriya, Tetsuichiro Saito, Takeshi Murata, Osamu Ohara, Yusuke Kawashima

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in ACS omega, 2026. 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. 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

10 authors.

Yasuomi MiyashitaDepartment of Applied Genomics, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.ORCID https://orcid.org/0009-0000-7874-8498
Ryo KonnoDepartment of Applied Genomics, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.ORCID https://orcid.org/0000-0002-4375-1133
Satoshi OgasawaraDepartment of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.
Yusei OkudaDepartment of Applied Genomics, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
Yuuki TakamukuDepartment of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.
Toshio MoriyaStructural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.ORCID https://orcid.org/0000-0001-7226-5487
Tetsuichiro SaitoDepartment of Developmental Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo, Chiba 260-8670, Japan.
Takeshi MurataDepartment of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.
Osamu OharaDepartment of Applied Genomics, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.ORCID https://orcid.org/0000-0002-3328-9571
Yusuke KawashimaDepartment of Applied Genomics, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.ORCID https://orcid.org/0000-0002-9779-8199

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Limited proteolysis mass spectrometry (LiP-MS) is a powerful approach for probing protein conformational changes on a proteome-wide scale. However, conventional workflows rely on a two-step digestion with proteinase K and trypsin, which increases complexity and reduces reproducibility and sensitivity. This study aimed to develop a simplified one-step protocol, termed Swift Trypsin LiP-MS (STLiP-MS), which uses a trypsin-immobilized spin column and high-speed centrifugation to achieve rapid and reproducible surface-limited proteolysis. Using HEK293 cell extracts, STLiP-MS identified 286 proteins exhibiting conformational changes upon phosphatase inhibition, including 37 enriched in phosphatase-related Gene Ontology categories. The method improvements, including suppression of predigestion and immediate enzyme inactivation, further increased sensitivity, enabling the detection of 799 proteins with structural alterations, of which 77 were enriched in phosphatase-related categories. Comparison with the single-pot solid-phase-enhanced sample preparation (SP3) method confirmed that these changes originated from structure-selective proteolysis and were not detectable under fully denaturing conditions. To demonstrate its broader applicability, we applied STLiP-MS to the adenosine A

Identifiers

PMID41552556
PMCPMC12809284

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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.