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Data-independent acquisition (DIA)-MS, utilizing hybrid spectral library search strategies, allows for the simultaneous quantification of thousands of proteins, showing promise in enhancing protein identification and quantification precision. However, low-quality profiles can considerably undermine quantitative precision, resulting in inaccurate protein quantification. To tackle this challenge, we introduced STAVER, a novel algorithm that leverages standardized benchmark datasets to reduce non-biological variation in large-scale DIA-MS analyses. By eliminating unwanted noise in MS signals, STAVER significantly improved protein quantification precision, especially in hybrid spectral library searches. Moreover, we validated STAVER\u2019s robustness and applicability across multiple large-scale DIA datasets, demonstrating significantly enhanced precision and reproducibility of protein quantification. STAVER offers an innovative and effective approach for enhancing the quality of large-scale DIA proteomic data, facilitating cross-platform and cross-laboratory comparative analyses. This advancement significantly enhances the consistency and reliability of findings in clinical research. The complete package is available at https:\/\/github.com\/Ran485\/STAVER.<\/jats:p>","DOI":"10.1093\/bib\/bbae553","type":"journal-article","created":{"date-parts":[[2024,11,6]],"date-time":"2024-11-06T19:32:49Z","timestamp":1730921569000},"source":"Crossref","is-referenced-by-count":4,"title":["STAVER: a standardized benchmark dataset-based algorithm for effective variation reduction in large-scale DIA-MS data"],"prefix":"10.1093","volume":"25","author":[{"given":"Peng","family":"Ran","sequence":"first","affiliation":[{"name":"Center for Cell and Gene Therapy , Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, , E301, School of Life Sciences, No. 2005, Songhu Road, Yangpu District, Shanghai 200438, P.R.","place":["China"]},{"name":"Fudan University , Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, State Key Laboratory of 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