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Protease- and Acid-catalyzed Labeling Workflows Employing 18O-enriched Water

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18O stable isotope labeling in MS-based proteomics.

Xiaoying Ye¹, Brian Luke, Thorkell Andresson

¹Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick Inc, NCI at Frederick, Frederick, MD 21702-1201, USA.

Briefings in Functional Genomics & Proteomics

|January 20, 2009

Summary

Stable isotope labeling using oxygen-18 (18O) facilitates quantitative proteomics by introducing mass shifts in peptides analyzed by mass spectrometry (MS). This technique aids in protein identification and quantitation across various research applications.

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Area of Science:

Proteomics
Analytical Chemistry
Biochemistry

Background:

Mass spectrometry (MS)-based proteomics utilizes stable isotope labeling for protein quantitation.
Differential (16)O/(18)O coding is a key technique for comparing protein abundance between samples.
This method relies on enzyme-catalyzed oxygen exchange at peptide C-termini using H(2)(18)O.

Purpose of the Study:

To review the application and utility of (16)O/(18)O labeling in mass spectrometry-based proteome research.
To examine different strategies employing (16)O/(18)O labeling for proteomic analysis.
To discuss analytical considerations and compare (16)O/(18)O labeling with alternative isotope-coding techniques.

Main Methods:

Enzyme-catalyzed oxygen exchange reaction using H(2)(18)O to label peptides.
Mass spectrometry analysis to detect mass shifts between (16)O and (18)O labeled peptides.
Comparative analysis of different (16)O/(18)O labeling strategies in proteomic workflows.

Main Results:

The (18)O exchange at the C-terminal carboxyl group introduces a specific mass shift, enabling peptide and protein identification and quantitation.
Strategies employing (16)O/(18)O labeling are effective for global comparative proteome profiling, targeted proteomics, PTM analysis, and biomarker discovery.
Analytical challenges such as variable (18)O exchange were identified, alongside a discussion of the technique's pros and cons.

Conclusions:

Differential (16)O/(18)O labeling is a valuable tool in MS-based proteomics for quantitative and qualitative analyses.
The technique offers versatile applications across various proteomic research areas.
Understanding its analytical nuances is crucial for optimal implementation and comparison with other isotope-coding methods.