Molecular & integrative analysis
Compare protein abundance and characterize HLA-associated peptide datasets with transparent evidence filters.
Analyses are tailored to your experimental design, data quality and research question. The workflow and deliverables are agreed following project review.
Analysis modules
Identification/quantification QC and missingness assessment.
Differential protein or peptide abundance.
Pathway and protein-network interpretation.
Post-translational modification analyses where measured.
HLA ligand length distributions and sequence motifs.
Peptide–HLA assignment and presentation-model comparisons.
Integration with transcriptomics or variant-derived candidates.
Data and metadata
Peptide/protein quantification and identification tables with confidence metrics; mzML or suitable raw MS data only when a complete processing workflow has been scoped; assay metadata and HLA information where relevant.
Proposed deliverables
Filtered protein/peptide tables; differential figures; ligand motif summaries; integrated evidence where applicable.
Interpretation and feasibility
Peptide identification, natural presentation and T-cell immunogenicity are distinct. MS false discovery rates, search databases and tool licences must be documented.
Methods and references
Methods, reference resources and software are selected for each project after protocol, feasibility and licence review. Applicable versions, references and interpretation limits are documented in the agreed workflow.