IsoformResolver

IsoformResolver performs peptide-centric protein inference for tandem mass spectrometry (MS/MS) data to resolve ambiguous protein identifications and summarize spectral counts for LC-MS/MS comparisons.

Key Features:

• Dual clustering strategy: Implements two clustering approaches—one based on peptides experimentally identified from MS/MS spectra and one based on an in silico digest of the protein database.
• Peptide-centric grouping: Groups proteins by shared peptides to present a minimal protein list while contextualizing proteins within all possible matches and avoiding redundant peptide listings.
• In silico digest clustering: Uses an in silico digest of the protein database to group functionally related proteins and provide stable identifiers for functional analysis and comparison.
• Spectral count summarization: Computes comprehensive spectral count summaries across protein groups to facilitate comparisons across multiple LC-MS/MS experiments.
• Protein relatedness and benchmarking: Examines relatedness of proteins within groups and enables performance comparisons with other protein inference software.

Scientific Applications:

• Protein inference in complex samples: Resolve ambiguous protein identifications in complex MS/MS datasets by organizing proteins around observed peptides.
• Comparative proteomics: Compare protein-level results across multiple LC-MS/MS experiments using spectral count summaries.
• Functional analysis: Support functional analysis and comparison using stable identifiers derived from in silico digest clustering.
• Method benchmarking: Assess and compare the performance of protein inference approaches against other protein inference software.

Methodology:

Performs dual clustering—(1) peptide-based clustering using experimentally identified MS/MS peptides and (2) clustering based on an in silico digest of the protein database—to construct peptide-centric protein groups, compute spectral count summaries, and evaluate protein relatedness and comparative performance versus other protein inference software.