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

Tobias JumelAndrej Shevchenko
Published in: Journal of proteome research (2024)
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.
Keyphrases
  • electronic health record
  • mass spectrometry
  • big data
  • machine learning
  • adverse drug
  • minimally invasive
  • data analysis
  • label free
  • transcription factor
  • deep learning