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bioRxiv · 10.1101/2023.08.28.555075

Multi-species benchmark analysis for LC-MS/MS validation and performance evaluation in bottom-up proteomics

Jumel, T.·Shevchenko, A.
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Abstract

We present an instrument-independent benchmarking procedure and software (LFQ_bout) for validation and comparative evaluation of the performance of LC-MS/MS and data processing workflows in bottom-up proteomics. It enables back-to-back comparison of common and emerging workflows, e.g. diaPASEF or ScanningSWATH, and evaluates the impact of arbitrary, inadequately documented settings or black-box data processing algorithms. The procedure enhances the overall performance and quantitative accuracy while enabling the detection of major error types.

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Jumel, T., Shevchenko, A.. 2023-08-29. Multi-species benchmark analysis for LC-MS/MS validation and performance evaluation in bottom-up proteomics. https://doi.org/10.1101/2023.08.28.555075

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