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SequenceAssembler: A tool for protein sequence assembly from mass spectrometry data
Celso Vitor A Q Calomeno1, Hulyana Brum2, Rodrigo S C Brant3
1Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz Paraná, Paraná, Brazil.
Journal of Proteomics
|October 10, 2025
Summary
SequenceAssembler (SA) software integrates peptide-spectrum matching and de novo sequencing data to reconstruct full-length proteins. This user-friendly tool enhances protein sequencing for biological research and biopharmaceutical development.
Area of Science:
- Proteomics
- Biotechnology
- Biopharmaceutical Development
Background:
- Accurate sequencing of complete proteoforms is crucial for understanding biological systems and advancing drug development.
- Current methods may lack integration for comprehensive protein sequence assembly.
Purpose of the Study:
- To introduce SequenceAssembler (SA), a software tool for assembling full-length protein sequences.
- To integrate peptide-spectrum matching (PSM) and de novo sequencing data for enhanced protein reconstruction.
Main Methods:
- Developed SequenceAssembler (SA) software with a user-friendly graphical interface.
- Integrated SA with established proteomics tools (Novor Cloud, PEAKS Studio, PatternLab for Proteomics).
- Validated SA by analyzing bovine serum albumin and trastuzumab using high-resolution mass spectrometry.
Main Results:
- SA successfully assembled full-length protein sequences by combining PSM and de novo sequencing data.
- Performance was comparable to existing tools like Stitch, with results dependent on parameter thresholds.
- Demonstrated ease of use with a streamlined workflow and one-click installation.
Conclusions:
- SequenceAssembler provides a unified platform for protein sequence assembly, addressing a gap in proteomics.
- The intuitive interface lowers adoption barriers, improving reproducibility and efficiency in core laboratories.
- SA facilitates rapid protein sequencing for diverse research applications.
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