specL

specL generates spectral libraries and assay panels for targeted proteomics to support SWATH and data-independent acquisition (DIA) workflows and precise peptide ion identification.

Key Features:

• BiblioSpec Reader: Imports spectral data from BiblioSpec files for integration into spectral libraries.
• Protein Information Integration: Adds protein annotations using FASTA-formatted amino acid sequence files.
• Export Functionality: Exports generated assay panels in formats compatible with Spectronaut.
• Assay Panel Generation: Provides functions to generate customizable assay panels from spectral libraries for SWATH and DIA analyses.

Scientific Applications:

• Targeted data extraction for SWATH and DIA: Supports extraction of peptide-specific MS coordinates (retention time, precursor and fragment masses) for SWATH and DIA workflows.
• Spectral library and assay panel creation: Produces spectral libraries and assay panels used for identification and targeted quantification of peptide ions.
• Reproducible quantitative proteomics: Enables generation of resources that improve reproducibility of quantitative peptide measurements in downstream analyses.

Methodology:

Implements import of BiblioSpec files, integration of FASTA protein sequences, generation of spectral libraries and customizable assay panels from existing spectral data, and export of Spectronaut-compatible assay panels; implemented in R.