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Updated: Apr 15, 2026

Identification of protein complexes with quantitative proteomics in S. cerevisiae

Identification of protein complexes with quantitative proteomics in S. cerevisiae

Published on: March 4, 2009

One-hour proteome analysis in yeast.

Alicia L Richards¹, Alexander S Hebert², Arne Ulbrich¹

¹1] The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA. [2] Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA.

Nature Protocols

|April 10, 2015

Summary

This summary is machine-generated.

This study presents an optimized proteomic profiling protocol using advanced chromatography and mass spectrometry (MS). The new method enhances protein identification in yeast, improving reproducibility and reducing analysis time.

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Last Updated: Apr 15, 2026

Identification of protein complexes with quantitative proteomics in S. cerevisiae

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Published on: March 4, 2009

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Area of Science:

Proteomics
Analytical Chemistry
Biochemistry

Background:

Recent advances in chromatography and mass spectrometry (MS) enable deep proteomic profiling.
Orbitrap hybrid mass spectrometers offer high performance for proteomic analysis.

Purpose of the Study:

To develop an optimized protocol for enhanced protein identification using Orbitrap hybrid mass spectrometry.
To reduce the need for extensive sample fractionation in proteomic studies.

Main Methods:

Optimized sample preparation including extensive bead beating for cell lysis.
Utilized 30-cm capillary columns with 1.7-μm bridged ethylene hybrid material.
Developed a column heater for specific flow rates (350-375 nl/min) in liquid chromatography-tandem MS (LC-MS/MS).

Main Results:

Identified up to 4,002 proteins in yeast (Saccharomyces cerevisiae) at a 1% false discovery rate (FDR).
Achieved 83% protein-level overlap in quintuplicate technical replicates, demonstrating high reproducibility.
The complete protocol, from cell lysis to database searching, takes approximately 24 hours.

Conclusions:

The developed protocol significantly increases protein identification in a single LC-MS/MS run.
This method offers a reproducible and time-efficient approach to deep proteomic profiling.
The protocol's aspects are adaptable for analyzing other organisms.