Supplementary Data: Finding Haplotypic Signatures in Proteins

Supplementary data related to the paper "Identifying Protein Haplotypes by Mass Spectrometry" <br> 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 <br> 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.

本数据集为论文《基于质谱鉴定蛋白质单倍型》（Identifying Protein Haplotypes by Mass Spectrometry）的补充数据。
SD1：包含所有目标蛋白质序列的FASTA文件（涵盖Ensembl参考蛋白质组、蛋白质单倍型序列、污染序列），不含诱饵序列。
SD2：包含所有目标与诱饵序列的FASTA文件。
SD3：包含所有肽段-谱匹配（peptide-spectrum matches, PSMs）的列表，附带全部相关元数据与质控措施。
SD4：包含已鉴定的氨基酸替换及其对应PSM编号的列表。
SD5：包含变异型PSM列表与PepQuery推荐的肽段候选物列表，附带每个肽段候选物的置信度评分。
若需复现后续处理流程，可使用发布于https://github.com/ProGenNo/IdentifyingHaplotypesByMS 的分析管线。该仓库还包含补充文件内容的详细说明。