Evidence map›Paper›PMID 42013821›Full record

ArticleJournal of proteome research2026

Evaluation of Data-Independent Acquisition-Based Phosphoproteomics Analysis in Mammalian and Bacterial Systems.

Sophie Hongfei Liu, Daniel H Call, Reta Birhanu Kitata, Issac K Attah, Rosalie K Chu, Marina A Gritsenko, Vishant Boradia, Christoph Grundner, Le Z Day, Jon M Jacobs

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Article in Journal of proteome research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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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

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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

10 authors.

Sophie Hongfei LiuPhysical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.
Daniel H CallEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.ORCID 0009-0007-5530-1598
Reta Birhanu KitataEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.ORCID 0000-0002-8973-7679
Issac K AttahEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.ORCID 0000-0002-9626-2069
Rosalie K ChuEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.
Marina A GritsenkoEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.
Vishant BoradiaCenter for Global Infectious Disease Research, Seattle Children's Research Institute, P. O. Box 5371, Seattle, Washington 98145-5005, United States.
Christoph GrundnerCenter for Global Infectious Disease Research, Seattle Children's Research Institute, P. O. Box 5371, Seattle, Washington 98145-5005, United States.ORCID 0000-0003-0596-6798
Le Z DayEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.
Jon M JacobsEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.ORCID 0000-0003-0557-7338

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Recent advancements in data-independent acquisition (DIA) workflows have greatly increased the depth and throughput of mass spectrometry-based proteomics. However, many of these advancements remain undercharacterized for phosphoproteomics, particularly in bacteria that have fewer protein phosphorylation events. We evaluated the impact of instrument/gradient length (Orbitrap Astral, 15 min; Orbitrap Exploris, 90 min), analysis tools (DIA-NN 1.9.2, DIA-NN 2.3, FragPipe, Spectronaut), and library search strategies (spectral-library versus library-free) on phosphoproteomic coverage and quantification in a human cell line and bacterial lysate. The 15 min Astral analysis identified similar numbers of phosphopeptides compared to a 90 min Exploris acquisition method across all analysis tools, demonstrating a substantial advantage in throughput. Within the Astral workflow, Spectronaut provided the highest phosphoproteome coverage, whereas DIA-NN 1.9.2, DIA-NN 2.3, and FragPipe exhibited less quantitative variation. We compared library-free and spectral-library search strategies using the

Indexed as

Bacterial ProteinsPhosphopeptidesPhosphoproteinsProteomeProteomicsHumansMass SpectrometryMycobacterium tuberculosisPhosphorylationBacterial ProteinsPhosphopeptidesPhosphoproteinsProteomeAstraldata-independent acquisitionDIA-NNFragPipelibrary-freemass spectrometryMycobacterium tuberculosisphosphoproteomicsspectral-librarySpectronaut

Identifiers

PMID42013821
PMCPMC13140600

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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.