Multispecies Benchmark Analysis for LC-MS/MS Validation and Performance 
Evaluation in Bottom-Up Proteomics.

Jumel, Tobias; Shevchenko, Andrej

doi:10.1021/acs.jproteome.3c00531

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Multispecies Benchmark Analysis for LC-MS/MS Validation and Performance Evaluation in Bottom-Up Proteomics.

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Shevchenko, Andrej
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

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Citation

Jumel, T., & Shevchenko, A. (2024). Multispecies Benchmark Analysis for LC-MS/MS Validation and Performance Evaluation in Bottom-Up Proteomics. Journal of proteome research, 23(2), 684-691. doi:10.1021/acs.jproteome.3c00531.

Cite as: https://hdl.handle.net/21.11116/0000-000F-15E4-8

Abstract

We present an instrument-independent benchmark procedure and software (LFQ_bout) for the validation and comparative evaluation of the performance of LC-MS/MS and data processing workflows in bottom-up proteomics. The procedure enables a back-to-back comparison of common and emerging workflows, e.g., diaPASEF or ScanningSWATH, and evaluates the impact of arbitrary and inadequately documented settings or black-box data processing algorithms. It enhances the overall performance and quantification accuracy by recognizing and reporting common quantification errors.