Evidence map›Paper›PMID 41696233›Full record

ArticleACS omega2026

Spectronaut and DIA-NN: A Comparison of their Performance in the Analysis of Lung Adenocarcinoma Biopsies.

Zhaoyan Yu, Anqi Du, Xiaona Xu, Yinan Li, Xiaoxue Ma, Wenyang Zhang, Yunzeng Zhang, Ivan K Chu, K W Michael Siu

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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. 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

9 authors.

Zhaoyan YuHuashan Hospital Affiliated to Fudan University, 12 Wulumuqi Road (M), Shanghai 200031, China.
Anqi DuCenter for Mass Spectrometry Research and Clinical Application, and Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center Affiliated to Shandong University, Lishan Campus, 46 Lishan Road, Jinan, Shandong 250013, China.
Xiaona XuCenter for Mass Spectrometry Research and Clinical Application, and Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center Affiliated to Shandong University, Lishan Campus, 46 Lishan Road, Jinan, Shandong 250013, China.
Yinan LiCenter for Mass Spectrometry Research and Clinical Application, and Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center Affiliated to Shandong University, Lishan Campus, 46 Lishan Road, Jinan, Shandong 250013, China.
Xiaoxue MaCenter for Mass Spectrometry Research and Clinical Application, and Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center Affiliated to Shandong University, Lishan Campus, 46 Lishan Road, Jinan, Shandong 250013, China.
Wenyang ZhangGuangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, 20 Jinying Road, Guangzhou, Guangdong 510640, China.
Yunzeng ZhangDepartment of Thoracic Surgery, Shandong Public Health Clinical Center Affiliated to Shandong University, Panlongshan Campus, 2999 Gangxing West Road, Jinan, Shandong 655442, China.
Ivan K ChuCenter for Mass Spectrometry Research and Clinical Application, and Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center Affiliated to Shandong University, Lishan Campus, 46 Lishan Road, Jinan, Shandong 250013, China.ORCID https://orcid.org/0000-0003-0652-975X
K W Michael SiuCenter for Mass Spectrometry Research and Clinical Application, and Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center Affiliated to Shandong University, Lishan Campus, 46 Lishan Road, Jinan, Shandong 250013, China.ORCID https://orcid.org/0000-0002-9551-6506

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Direct data-independent acquisition (DIA) in liquid chromatography-tandem mass spectrometry (LC-MS/MS) has developed into a powerful methodology for proteomics. Herein, we directly compare the performance of two widely used DIA computational platformsSpectronaut and DIA-NNusing paired tumor and peritumor tissue biopsies from human lung carcinoma (LUAD) patients, samples that one would encounter in a clinical research lab in a hospital setting. The evaluations include the following: (1) protein identification depth, (2) quantitative consistency, and (3) differential expression on the same set of LC-MS/MS runs, using nominally identical computational parameters and settings. Both Spectronaut and DIA-NN identified ∼>7600 proteins in the LUAD samples, with 7180 proteins common to both platforms. Spectronaut reported 1250 upregulated proteins and 266 downregulated proteins (tumor versus peritumor), while DIA-NN reported 1819 and 174 proteins, respectively. A total of 1130 differentially expressed proteins (DEPs) were common to both platforms. Of the top 50 DEPs, 34 were shared between Spectronaut and DIA-NN. Two of these DEPsHSPA5 and CAV1were also among the top 50 proteins showing the highest degrees of protein-protein interaction. The DEPs enabled classification of the LUAD patients into three subtypes; the clinical validity of the current subtypes will need to be substantiated in the future with additional LUAD samples and experimentation.

Identifiers

PMID41696233
PMCPMC12903166

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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.