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Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm
Brian C Searle1, Surendra Dasari, Phillip A Wilmarth
1Department of Pediatrics and School of Dentistry, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, USA.
Journal of Proteome Research
|April 13, 2005
Summary
A new algorithm, OpenSea, effectively identifies protein modifications from mass spectrometry data. This method discovered 80 modifications, including 36 novel ones in human eye tissue, aiding biological interpretation.
Area of Science:
- Biochemistry
- Proteomics
- Bioinformatics
Background:
- Robust identification of post-translational protein modifications is crucial for data mining and biological insights.
- Existing methods require improvement for high-throughput analysis of complex biological samples.
Purpose of the Study:
- To evaluate the efficacy of the OpenSea mass-based alignment algorithm for identifying post-translational modifications (PTMs) in a high-throughput setting.
- To explore the utility of OpenSea in analyzing complex protein digests from human cataractous lens tissue.
Main Methods:
- Utilized two-dimensional liquid chromatography coupled with mass spectrometry (high and low mass accuracy).
- Employed automated de novo sequencing followed by OpenSea mass-based sequence alignment.
- Analyzed protein digests from human cataractous lens, a tissue rich in modified proteins.
Main Results:
- Successfully identified a total of 80 protein modifications.
- Discovered 36 previously unreported modifications in the human lens.
- Demonstrated OpenSea's capability in a high-throughput environment for PTM detection.
Conclusions:
- The OpenSea algorithm robustly identifies post-translational modifications from mass spectrometry data.
- Automated data processing with OpenSea facilitates the discovery of numerous known and novel protein modifications.
- This approach enhances the potential for comprehensive proteomic analysis and biological interpretation.