ArticleNature communications2023
Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
What it found
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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.
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Who cites it
81 citing papers in PubMed, 124 citations in OpenAlex.
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- LC-HRMS and Molecular Networking for Non-Targeted Screening of Emerging Contaminants in Cosmetics: Workflow, Applications, and Regulatory Challenges.Molecules (Basel, Switzerland) · 2026Review
- Trends in Computational Metabolomics: A Perspective on Five Years of Software Development, Challenges, and Opportunities (2021-2025).Analytical chemistry · 2026Review
- AlphaDIA enables DIA transfer learning for feature-free proteomics.Nature biotechnology · 2026Article
- dia-PASEF Enables Rapid Profiling of the Human Secretome for Deeper Insights Into Cellular Dynamics and Inflammatory Mechanisms.Molecular & cellular proteomics : MCP · 2026Article
- Sirtuin 1 Activation Mitigates Murine Vasculitis Severity by Promoting Mitophagy.Circulation research · 2026Article
- Functional impact of high-altitude hypoxia on central nervous system drug transport: integrated analysis of blood-brain barrier permeability, drug transporter/enzyme expression, and pharmacokinetics.Fluids and barriers of the CNS · 2026Article
- Ground Truth-Based Evaluation of False Discovery Rate and Statistical Power in DIA Proteomics.bioRxiv : the preprint server for biology · 2026Article
- Clarifying the scope and capabilities of ROTS in differential expression analysis.Bioinformatics (Oxford, England) · 2026Article
- What Are the Practical Applications of Single-Cell Proteomics?Proteomes · 2026Article
- Noninvasive early detection and grading of pneumoconiosis via plasma proteomics and machine learning: PRSS3 as a potential biomarker.Clinical proteomics · 2026Article
- Evaluation of Data-Independent Acquisition-Based Phosphoproteomics Analysis in Mammalian and Bacterial Systems.Journal of proteome research · 2026Article
- Multi-omics analysis identified serumJournal of thoracic disease · 2026Article
- Comprehensive top-down mass spectral repository enables pan-dataset analysis and top-down spectral prediction.bioRxiv : the preprint server for biology · 2026Article
- Distinct Proteomic Signatures Driving Progression of Sarcopenia: A Longitudinal Multicohort Study.Journal of cachexia, sarcopenia and muscle · 2026Article
- Exploring an Intermediate Colorectal Cancer Screening Test Based on Stool Proteomics and Machine Learning for Optimizing the Selection of Patients for Colonoscopy Identified From FIT.Molecular & cellular proteomics : MCP · 2026Article
- Pho-Tip: One-Pot Dephosphorylation for Rapid and Sensitive Analysis of DIA Phosphoproteomics Data.Analytical chemistry · 2026Article
- Proteoforms as the true units of physiological function.European journal of applied physiology · 2026Review
- Advancing DIA-Based Limited Proteolysis Workflows: Introducing DIA-LiPA.Analytical chemistry · 2026Article
21 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A plethora of software suites and multiple classes of spectral libraries have been developed to enhance the depth and robustness of data-independent acquisition (DIA) data processing. However, how the combination of a DIA software tool and a spectral library impacts the outcome of DIA proteomics and phosphoproteomics data analysis has been rarely investigated using benchmark data that mimics biological complexity. In this study, we create DIA benchmark data sets simulating the regulation of thousands of proteins in a complex background, which are collected on both an Orbitrap and a timsTOF instruments. We evaluate four commonly used software suites (DIA-NN, Spectronaut, MaxDIA and Skyline) combined with seven different spectral libraries in global proteome analysis. Moreover, we assess their performances in analyzing phosphopeptide standards and TNF-α-induced phosphoproteome regulation. Our study provides a practical guidance on how to construct a robust data analysis pipeline for different proteomics studies implementing the DIA technique.
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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 Socratic graph.