Supplementary Data: Finding Haplotypic Signatures in Proteins

Supplementary data related to the paper "Identifying Protein Haplotypes by Mass Spectrometry" SD1: FASTA file including all target protein sequences (Ensembl reference proteome, protein haplotype sequences, contaminant sequences), excluding decoys SD2: FASTA file including all target and decoy sequences SD3: List of all peptide-spectrum matches (PSMs) with all related metadata and quality control measures SD4: List of substitutions identified, along with IDs of corresponding PSMs SD5: List of variant PSMs and peptide candidates suggested by PepQuery, along with confidence scores for each peptide candidate To reproduce the post-processing steps, you can use the pipeline published at https://github.com/ProGenNo/IdentifyingHaplotypesByMS The repository also contains additional explanations of supplementary files contents.