Blind Search for Protein Modifications Using Mass Spectrometry
Author Information
Author(s): Barsnes Harald, Mikalsen Svein-Ole, Eidhammer Ingvar
Primary Institution: Department of Informatics, University of Bergen
Hypothesis
Can a blind search algorithm effectively identify post-translational modifications and amino acid substitutions in proteins using peptide mass fingerprints?
Conclusion
The developed algorithm can indicate post-translational modifications or amino acid substitutions in proteins without prior assumptions.
Supporting Evidence
- The algorithm can suggest areas where mass shifts may occur in overlapping peptides.
- MassShiftFinder is designed for low-throughput characterization of single proteins.
- The method allows for the detection of both known and unknown modifications.
Takeaway
Scientists created a computer program that helps find changes in proteins by looking at their mass. This can help understand how proteins work better.
Methodology
The study developed an algorithm and software tool, MassShiftFinder, that performs a blind search using peptide mass fingerprints from two proteases.
Potential Biases
The likelihood of finding artifacts increases with the number of non-identified peptides.
Limitations
The algorithm's effectiveness depends on good experimental sequence coverage and overlapping peptides.
Digital Object Identifier (DOI)
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