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Detailed peptide characterization using PEPTIDEMASS--a World-Wide-Web-accessible tool
M R Wilkins1, I Lindskog, E Gasteiger
1Central Clinical Chemistry Laboratory, Geneva University Hospital, Switzerland. marc.wilkins@dim.hcuge.ch
Electrophoresis
|March 1, 1997
Summary
Unexplained peptide masses in fingerprinting can stem from various sources. The PEPTIDEMASS program aids researchers by generating theoretical peptide masses from annotated protein databases, simplifying data interpretation.
Area of Science:
- Proteomics
- Bioinformatics
- Computational Biology
Background:
- Peptide mass fingerprinting (PMF) frequently yields unexplained peptide masses.
- Potential causes include missed cleavages, incomplete reduction/alkylation, protein modifications, database errors, splicing variants, or artifacts.
- Verifying these discrepancies is often labor-intensive.
Purpose of the Study:
- To develop a computational tool for better utilization of annotated protein databases in understanding PMF data.
- To automate the generation of theoretical peptide masses, accounting for protein annotations.
Main Methods:
- The PEPTIDEMASS program was developed to generate theoretical peptide masses.
- It processes proteins from the SWISS-PROT database or user-provided sequences.
- The program incorporates SWISS-PROT annotations, including signal peptides, propeptides, transit peptides, post-translational modifications, and disulfide bonds.
Main Results:
- PEPTIDEMASS generates predicted peptide masses for specified protein sequences.
- It accounts for known protein features and modifications present in SWISS-PROT annotations.
- The program alerts users to potential mass variations due to isoforms, database conflicts, or splicing variations.
Conclusions:
- PEPTIDEMASS facilitates the interpretation of complex PMF data by providing theoretical mass predictions.
- It aids in identifying and verifying potential causes for unexplained peptide masses.
- The tool is freely accessible, supporting the broader scientific community in proteomics research.