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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
Published on: November 15, 2017
Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass
Masaya Ono1, Miki Shitashige, Kazufumi Honda
1Chemotherapy Division and Cancer Proteomics Project, National Cancer Center Research Institute, Tokyo 104-0045, Japan.
Molecular & Cellular Proteomics : MCP
|March 23, 2006
Summary
We created a new platform for analyzing protein expression using nanoflow liquid chromatography-mass spectrometry (LC-MS). This system enhances data analysis for proteomics research.
Area of Science:
- Proteomics
- Analytical Chemistry
- Biochemistry
Background:
- Differential protein expression analysis is crucial for understanding biological processes.
- High-throughput proteomics requires robust and reproducible analytical platforms.
- Existing methods face challenges in data handling and quantification accuracy.
Purpose of the Study:
- To develop an integrated platform for analyzing large datasets from nanoflow LC-MS.
- To improve differential protein expression analysis in proteomics.
- To provide a reliable tool for experimental and translational proteomics.
Main Methods:
- Developed an integrated system of hardware and software modules.
- Utilized nanoflow liquid chromatography (LC) coupled with mass spectrometry (MS).
- Employed a hybrid Q-TOF mass spectrometer for high-speed data acquisition (1s spectra).
- Implemented a dynamic programming algorithm for nano-LC time jitter correction.
Main Results:
- Achieved comprehensive protein peak detection (60,000-160,000 peaks).
- Demonstrated high reproducibility (CV 0.35-0.39, R² > 0.92).
- Enabled accurate quantification over a wide dynamic range (>10^3).
Conclusions:
- The developed platform effectively handles vast data from nanoflow LC-MS.
- The system offers high comprehensiveness, reproducibility, and quantification accuracy.
- This platform is suitable for diverse applications in experimental and translational proteomics.
