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May 25, 2026Analytical Chemistry

ProteoIntegrator: A Scalable and Integrated Platform for Robust Multi-Source Proteomics Data Harmonization, Differential and Functional Analysis

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Authors

YRYan RenChinese Academy of SciencesZSZhaomei ShiShanghaiTech UniversityDCDan ChenMerit Network

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Implication

Randomized trial benchmarks innovative platform that harmonizes proteomics data, highlighting its effectiveness for robust analysis.

Key Points

  • This research aims to present ProteoIntegrator, a platform for harmonizing and analyzing multi-source proteomics data efficiently.
  • Developed a web-based tool to automate quality control and differential expression analysis.
  • Benchmarking of 12 imputation methods, including Bayesian principal component analysis and ComBat.
  • Conducted performance evaluation on over 1000 samples across multiple instruments.
  • Identified BPCA combined with ComBat as optimal for batch correction with >98% quantification accuracy.
  • Demonstrated successful detection of differentially expressed proteins, outperforming HarmonizR.
  • Validated utility with reanalysis of kidney cancer datasets showing significant metabolic shifts.

Cite This Study

Ren et al. (2026) studied this question.

synapsesocial.com/papers/6a13e8680e02ee3982d33290https://doi.org/10.1021/acs.analchem.6c00082
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Also Consider

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  1. 1Missing value estimation methods for DNA microarrays2001 · 4,372 citations
  2. 2NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses2020 · 175 citations
  3. 3HarmonizR enables data harmonization across independent proteomic datasets with appropriate handling of missing values2022 · 76 citations
  4. 4Missing Value Imputation Approach for Mass Spectrometry-based Metabolomics Data2018 · 715 citations
  5. 5GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies2018 · 181 citations