Neopeptide Analyser

Neopeptide Analyser identifies and quantifies neopeptides—peptides generated by native protein cleavage rather than enzymatic digestion (e.g., trypsin)—in mass spectrometry proteomics datasets to enable detection of disease-associated proteolytic events and support biomarker discovery.

Key Features:

• Integration with Progenesis QIP: Operates in conjunction with the label-free MS quantification tool Progenesis QIP to process mass spectrometry quantification data.
• Neopeptide Identification: Filters and identifies neopeptide sequences by detecting peptide termini not generated by trypsin digestion.
• Adjacent Residue Annotation: Reports residues adjacent to identified neopeptides within their parent protein sequences to provide peptide context.
• Quantification and Statistical Analysis: Normalizes neopeptide quantification values and performs statistical tests to support robust comparative analyses.

Scientific Applications:

• Disease Pathology Analysis: Identifies neopeptides associated with pathological conditions to inform understanding of disease mechanisms.
• Biomarker Discovery: Aids identification of potential diagnostic biomarkers, including candidates relevant to osteoarthritis.
• Identification of Treatment Targets: Reveals peptides and cleavage events involved in extracellular matrix degradation and matrix turnover that may indicate novel therapeutic targets.

Methodology:

Automates neopeptide filtering and identification, annotates adjacent residues, normalizes quantification values, performs statistical testing, and integrates with Progenesis QIP to process label-free MS quantification data.