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This research aims to systematically evaluate the performance of various PASEF acquisition strategies in complex metaproteomes.

August 5, 2026Nature CommunicationsOpen Access

Systematic evaluation of PASEF acquisition strategies in complex metaproteomes

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Systematic evaluation benchmarks five PASEF modes in complex metaproteomes, revealing effective strategies.

This research aims to systematically evaluate the performance of various PASEF acquisition strategies in complex metaproteomes.
Benchmarking five PASEF modes (DDA-, DIA-, Slice-, Synchro-, and midia-PASEF) using a complex fecal peptide background.
Conducted 540 LC–MS acquisitions across three gradients and input levels under matched conditions.
Performance assessed using data-derived scores for peptide and protein coverage.
DIA-based strategies significantly outperform DDA-PASEF in peptide and protein coverage, especially for low-abundance features.
DIA- and Slice-PASEF exhibit strong quantitative reproducibility and reduced ratio compression.
Functional profiling using the top methods captures consistent host and microbial responses in a murine colonic injury model.

Xian et al. (2026) studied this question.

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