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A computer program to aid the sequencing of peptides in collision-activated decomposition experiments
J Fernández-de-Cossío1, J Gonzalez, V Besada
1Division of Automation, Center for Genetic Engineering and Biotechnology, Havana, Cuba.
Computer Applications in the Biosciences : CABIOS
|August 1, 1995
Summary
A new computer program, MSEQ, uses graph theory to help sequence peptides from mass spectrometry data. This tool accurately identifies peptide sequences, even distinguishing similar amino acids, aiding proteomic research.
Area of Science:
- Proteomics
- Computational Biology
- Mass Spectrometry
Background:
- Peptide sequencing is crucial for understanding protein function.
- Analyzing collision-activated decomposition (CAD) spectra can be complex.
- Existing methods may struggle with isobaric amino acids and spectral interpretation.
Purpose of the Study:
- To introduce MSEQ, a novel computer program for peptide sequencing.
- To leverage graph theory for efficient and accurate sequence determination from CAD spectra.
- To improve the identification of peptide sequences, including those with isobaric amino acids.
Main Methods:
- Developed MSEQ based on graph theory principles.
- Input data includes peptide molecular weight, daughter ion masses, and terminal group masses.
- Utilized a probability model derived from extensive CAD spectral data.
Main Results:
- MSEQ outputs ranked peptide sequences with scores and daughter ion assignments.
- The program successfully sequenced numerous peptides, with correct sequences often ranking in the top five.
- MSEQ can differentiate isobaric amino acids like leucine and isoleucine based on fragmentation patterns.
Conclusions:
- MSEQ is an effective and efficient tool for peptide sequencing using CAD mass spectrometry data.
- The program's ability to handle complex spectra and distinguish isobaric amino acids enhances its utility in proteomics.
- MSEQ offers a fast, memory-efficient solution for peptide sequence analysis.