lutefisk

Lutefisk performs de novo peptide sequencing from tandem mass spectrometry (MS/MS) data to infer peptide sequences and detect novel peptides or sequence variants, including those arising from post-translational modifications.

Key Features:

• De novo sequencing: Performs automatic deduction of peptide sequences directly from MS/MS spectra without relying on sequence databases.
• Ambiguity handling: Implements a modified FASTA algorithm adapted to address sequence ambiguities inherent in tandem MS/MS data.
• Homologous nonexact search support: Enables homologous, nonexact searches by producing sequences suitable for downstream database comparison.

Scientific Applications:

• Novel peptide identification: Identification of peptides absent from existing protein and peptide databases.
• Non-model organism proteomics: Characterization of proteins from non-model organisms or newly discovered species lacking reference sequences.
• PTM and complex-sample analysis: Analysis of complex biological samples where post-translational modifications or ambiguous spectra impede database matching.

Methodology:

Performs de novo sequencing from tandem MS/MS spectra and applies a modified FASTA algorithm to handle sequence ambiguities and enable homologous nonexact database searches; generated sequences are available for downstream homologous searches.