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Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
Published on: November 13, 2021
Analysis of human liver proteome using replicate shotgun strategy
Ming Chen1, Wantao Ying, Yanping Song
1Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, PR China.
Proteomics
|July 12, 2007
Summary
This study comprehensively mapped the human liver proteome using a liquid-based shotgun strategy, identifying over 13,000 proteins. The advanced method revealed a dynamic range of nine orders of magnitude for protein expression.
Area of Science:
- Proteomics
- Human Liver Biology
- Mass Spectrometry
Background:
- The human liver proteome is complex and incompletely characterized.
- Comprehensive protein identification is crucial for understanding liver function and disease.
Purpose of the Study:
- To develop and apply a liquid-based shotgun strategy for comprehensive human liver proteome identification.
- To identify a significant portion of the human liver proteome, including low-abundance proteins.
Main Methods:
- Proteins extracted from human liver tissue and digested.
- Off-line strong cation exchange (SCX) chromatography coupled with RPLC-MS/MS.
- Data-dependent MS/MS spectra acquisition and analysis using strict filter criteria.
Main Results:
- Identification of 13,150 nonredundant proteins, representing 48.42% of the predicted human proteome.
- High-confidence dataset of 7,001 proteins identified by two or more peptides.
- Detection of a large number of low-abundance proteins, with a dynamic range of at least nine orders of magnitude.
Conclusions:
- The liquid-based shotgun strategy provides a comprehensive approach to human liver proteome analysis.
- The study significantly expands the catalog of identified human liver proteins.
- The findings offer a valuable resource for future research in liver biology and disease.
