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Quantitative proteomics using 16O/18O labeling and linear ion trap mass spectrometry
Daniel López-Ferrer1, Antonio Ramos-Fernández, Salvador Martínez-Bartolomé
1Protein Chemistry and Proteomics Laboratory, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
Proteomics
|March 15, 2006
Summary
This study shows that oxygen-18 (18O) labeling can be used for accurate, large-scale proteome quantification with linear ion trap mass spectrometry. This method allows for reliable identification and quantification of proteins from small samples.
Area of Science:
- Proteomics
- Mass Spectrometry
- Biochemistry
Background:
- Quantitative proteomics relies on methods like stable isotopic labeling.
- Oxygen-16/oxygen-18 (16O/18O) labeling offers advantages but typically requires high-resolution mass spectrometers due to small mass differences.
Purpose of the Study:
- To investigate the feasibility of using 16O/18O labeling with linear ion trap (IT) mass spectrometry for large-scale quantitative proteome analysis.
- To develop and validate a protocol for accurate quantitative proteomics using this approach.
Main Methods:
- A protocol involving protein digestion, desalting, 16O/18O labeling, mass spectrometry (MS), and quantitative analysis was established.
- The method was tested using protein standards and whole proteome extracts from mesenchymal stem cells.
Main Results:
- The study successfully identified and quantified 140 proteins from a 10 µg proteome extract.
- Relative expression changes greater than twofold were identified with 95% confidence.
Conclusions:
- Accurate quantitative proteome analysis using 16O/18O labeling is achievable with linear IT MS.
- This method does not compromise large-scale peptide identification efficiency, making it practical for widespread use.