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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Data from quantitative label free proteomics analysis of rat spleen
Khadar Dudekula1, Thierry Le Bihan1
1SynthSys, University of Edinburgh, Waddington Building, The King׳s Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom.
Data in Brief
|July 1, 2016
Summary
This study optimized label-free quantitative proteomic analysis of rat spleen using robust protein extraction and liquid chromatography-tandem mass spectrometry (LC-MS-MS). Fractionation methods were compared, revealing optimal strategies for identifying spleen proteins.
Area of Science:
- Proteomics
- Biochemistry
- Animal Models
Background:
- Label-free quantitative proteomic analysis is crucial for understanding biological systems.
- Rat spleen is a complex organ with diverse protein expression.
Purpose of the Study:
- To develop and optimize a robust method for protein extraction and LC-MS-MS analysis of rat spleen.
- To compare different protein fractionation strategies for enhanced proteomic depth.
- To establish a reliable dataset for future quantitative proteomic studies.
Main Methods:
- Label-free quantitative proteomic analysis of rat spleen tissue.
- Development of a urea and SDS-based buffer for protein extraction.
- Comparison of non-fractionated versus SDS-PAGE fractionation (3 and 5 fractions) prior to LC-MS-MS analysis.
Main Results:
- Identification of 3484 unique proteins across all experiments (2460 with at least two peptides).
- SDS-PAGE fractionation into five fractions yielded the highest protein identification (2864 proteins).
- Established a comprehensive protein list and quantitative variability data based on fractionation strategies.
Conclusions:
- Optimized protein extraction and LC-MS-MS protocols enhance proteomic analysis of rat spleen.
- SDS-PAGE fractionation significantly increases protein identification depth.
- The generated dataset provides a foundation for future quantitative proteomic studies and experimental design.
