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

Overview

Journal J Proteome Res

Publisher American Chemical Society

Specialty Biochemistry

Date 2024 Jan 20

PMID 38243904

Authors

Tobias Jumel

Andrej Shevchenko

Affiliations

Soon will be listed here.

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, ., 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.

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