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Reference Yeast and Human Whole Cell Protein Extracts for Mass Spectrometry Instrument Performance Monitoring and Method Development

Part # PS218

Abstract

Sergei Saveliev, Ethan Strauss, Mike Rosenblatt and Marjeta Urh
Promega Corporation, Madison, WI sergei.saveliev@promega.com

To monitor mass spec instrument performance for proteomics applications and optimize protein mass spec sample preparation, a reference protein material of high complexity is required. Whole cell protein extracts provide this desired sample complexity. However, to be compatible with mass spec applications, such extracts should meet a number of design requirements:
• compatibility with LC/MS (free of detergents, etc.)
• high protein integrity (minimal level of protein degradation and nonbiological
PTMs)
• compatibility with common sample preparation methods such as proteolysis, PTM enrichment and mass-tag labeling
• Lot-to-lot reproducibility
Here we describe whole cell protein extracts from yeast and human cells that meet the above criteria. Two extract formats have been developed:
• Pre-digested extracts (peptides); primary use - instrument performance monitoring
• Intact protein extracts; primary use – optimization of sample preparation

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