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Protein identification in DNA databases by peptide mass fingerprinting
P James1, M Quadroni, E Carafoli
1Department of Biology, Swiss Federal Institute of Technology (ETH), Zürich.
Protein Science : a Publication of the Protein Society
|August 1, 1994
Summary
This study introduces a novel multidimensional search method for protein identification using peptide fragment weights. This approach enhances identification confidence, enabling DNA database searches and linking proteomics with genomics.
Area of Science:
- Proteomics
- Bioinformatics
- Genomics
Background:
- Protein identification traditionally relies on searching protein databases with peptide fragment weights.
- Limitations exist in current methods for high-confidence identification and integration with genomic data.
Purpose of the Study:
- To present a novel multidimensional search method for protein identification.
- To increase the confidence level of protein identification.
- To enable the examination of DNA sequence databases for protein identification.
Main Methods:
- Utilizing multidimensional searches based on peptide fragment weights.
- Replacing protein sequences with calculated fragment weights for various cleavage methods.
- Searching DNA sequence databases using mass profiles.
Main Results:
- Significantly increased confidence levels for protein identification.
- Enabled direct searching of DNA sequence databases.
- Established a link between 2-dimensional gel electrophoresis protein databases and genome sequencing projects.
- Facilitated matching unknown proteins to expressed sequence tags.
Conclusions:
- The multidimensional search method offers a robust approach for high-confidence protein identification.
- This method bridges proteomics and genomics, potentially reducing the need for sequencing cloned proteins.
- A free automated server for mass profile database searching is available.