PEAKS Studio 13: Advanced Proteomics Software for DDA & DIA

PEAKS Studio 13 is the latest version of Bioinformatics Solutions Inc.'s flagship proteomics software, released in June 2025 . It features redesigned DDA and DIA workflows, unmatched DIA performance with SPIDER for novel peptide discovery, expanded quantification options, and a new Transition List Generator for targeted proteomics .

Key New Features in Version 13

Redesigned Workflows

• Streamlined DDA & DIA Workflows: Fully redesigned for smoother, more flexible user experience; choose where to end analysis or add steps later without starting over

• DIA Peptidome Workflow: Enhanced with GraphNovo deep learning sequencing algorithm and sequence variant analysis

Unmatched DIA Performance

• Faster Processing: CPU and GPU speeds significantly improved; analysis speed increased several times

• DIA SPIDER: Discover novel peptides and sequence variants across species, unlocking the "dark proteome" — peptides not in reference databases

• Full Result Transparency: New Feature tab displays all MS1 features associated with each peptide identification for interactive validation

Expanded Quantification

• Multiple Methods: Support for Top3 and MaxLFQ alongside labeled and label-free quantification

• Broader Application: PTM, SPIDER, and PRM quantification now supported

Targeted Proteomics Tools

• Transition List Generator: New tool to generate ion pair lists directly from PEAKS results or theoretical FASTA digest for targeted assays

• Enhanced PRM: Support for PRM PASEF, SILAC-labeled PRM, and timsTOF PRM data; new PRM protein annotation

DDA Enhancements

• Quantification Integration: PEAKS PTM and SPIDER identification results can now be used for quantitative analysis

• New Filter: "Found by" filter added to peptide lists

Additional Improvements

• Flexible FDR Control: Optional precursor FDR/score threshold application for result filtering

• Optimized Scoring: Improved protein and peptide scoring increases identification confidence