MS1Connect

MS1Connect computes similarity scores between pairs of mass spectrometry (MS) runs using intact peptide (MS1) scans to identify related datasets and support comparative proteomics and species origin prediction.

Key Features:

• Similarity calculation: Computes similarity scores between two MS runs based on MS1 (intact peptide) data.
• Intact peptide (MS1) scan analysis: Focuses on MS1 scans rather than fragment (MS2) scans to derive similarity metrics.
• Robustness to protocol variation: Enables assessment of similarity across datasets acquired using different experimental protocols without requiring direct comparison of fragmentation patterns.
• Species prediction accuracy: Demonstrates superior performance in predicting species origin of proteomics samples compared to baseline methods.
• Correlation with MS2-derived similarities: Produces MS1-based similarity scores that correlate highly with similarities derived from MS2 scans.

Scientific Applications:

• Proteomics research: Facilitates identification of relevant MS datasets for comparative proteomics analyses.
• Biodiversity and taxonomy studies: Supports species-origin assignment in proteomics-based biodiversity and taxonomic investigations.
• Data integration and reproducibility: Aids comparison and integration of datasets acquired under different experimental conditions to improve reproducibility.

Methodology:

Computes similarity scores between pairs of MS runs using features extracted from intact peptide (MS1) scans; performance was assessed by comparing species prediction accuracy to baseline methods and by correlating MS1-derived scores with MS2-derived similarities.