Stitch

Stitch performs template-based assembly of proteomics short reads to enable de novo antibody sequencing and antibody repertoire profiling.

Key Features:

• Template-based assembly: Assembles proteomics short reads against templates to reconstruct complete antibody sequences.
• Mass-based alignment algorithm: Uses a mass-based alignment that explicitly accounts for mass coincidence errors to improve peptide sequence assembly accuracy.
• Isobaric residue assignment: Applies a postprocessing procedure using secondary fragments (satellite ions, e.g., w-ions) to distinguish leucine (L) and isoleucine (I).
• Expanded input compatibility: Accepts de novo peptide sequencing outputs from Casanovo, PEAKS, Novor.Cloud, pNovo, and MaxNovo, as well as flat text and FASTA formats.
• Integrated spectrum viewer: Provides spectrum visualization to evaluate and validate evidence for sequence assignments.

Scientific Applications:

• De novo antibody sequencing: Reconstruction of antibody amino acid sequences directly from bottom-up proteomics data.
• Antibody repertoire profiling: Profiling of antibody sequence diversity within samples using assembled peptide reads.
• Immunological research and vaccine development: Accurate antibody characterization to inform immunology studies and vaccine design.
• Therapeutic antibody design and characterization: Support for precise sequence determination relevant to therapeutic antibody development.

Methodology:

Template-based assembly of proteomics short reads, a mass-based alignment algorithm accounting for mass coincidence errors, postprocessing for L/I assignment using satellite (w-) ions, support for inputs from Casanovo, PEAKS, Novor.Cloud, pNovo, MaxNovo, flat text and FASTA, and spectrum visualization for validation.