Finding Haplotypic Signatures in Proteins

Code related to the "Finding Haplotypic Signatures in Proteins" publication: https://doi.org/10.1101/2022.11.21.517096

Requirements and Usage

Required software is Snakemake and Conda, remaining libraries are included in the provided Conda environment, created automatically by Snakemake.

Steps for reproducing results:

• Download supplementary data from https://doi.org/10.6084/m9.figshare.21408117.v1
• Clone this repository
• Provide path to the downloaded files following instructions config.yaml
• For generating mirrored plots, a rerun of MS2PIP is necessary. This step can be skipped to re-generate the remaining results.
• Run the pipeline using snakemake -c<# cores> -p --use-conda

Additional files provided

Two additional files were derived from data made public by Spooner et al. [1]

• protein_haplotypes_1.csv: List of protein haplotypes created using alleles with minor allele frequency (MAF) > 0.01
• substitutions_list.tsv: List of substitutions found in the provided haplotypes, along with other pre-computed values

Supplementary data format

Description of supplementary data accessible at https://doi.org/10.6084/m9.figshare.21408117.v1:

SD1 and SD2: protein databases in the FASTA format:

>tag|accession|description
PROTEINSEQUENCE

SD3: CSV, list of all resulting PSMs with confidence metrics. The included columns are:

• PSMId: artificial identifier of the peptide-spectrum match
• SpectrumTitle: identifier of the matching spectrum, as given in the data set
• Proteins: accession identifiers of the matching protein sequences
• Position: positions of the peptide within the respective protein
• Sequence: sequence of the peptide without post-translational modifications (PTMs)
• Peptide: sequence of the peptide with possible PTMs
• sample_ID: identifier of the sample as given in the data set
• fragment_ID: identifier of the sample fragment as given in the data set
• measured_rt: measured retention time (RT)
• rt_Abs_error: absolute distance between measured and predicted RT
• spectra_cos_similarity: cosine similarity between matching peaks in the observed and predicted spectrum
• spectra_angular_similarity: angular similarity between matching peaks in the observed and predicted spectrum
• score: PSM score obtained from Percolator
• q-value: q-value obtained from Percolator
• posterior_error_prob: posterior error probability obtained from Percolator

SD4: list of identified amino acid substitutions, tab-separated

• ProteinVariant: amino acid substitution description
• Peptide: list of peptide sequences where the substitution has been identified, separated by semicolon
• PeptideType: type of the respected peptide
• PSMId: IDs of PSMs where this substitution has been identified
• Samples: IDs of respective samples

SD5: list of all variant PSMs and PepQuery validation, comma-separated

• PSMId: artificial identifier of the peptide-spectrum match (MAtching with SD3)
• PepQuery_class: classification by PepQuery: confident, better_ref_pep_with_mod, better_ref_pep or low_score
• posterior_error_prob: PEP value assigned to the variant match by Percolator
• xtandem_sequence: Matched variant sequence obtained from the X!Tandem search, including modifications (Unimod ID in the sequence)
• PepQuery_sequence: Canonical peptide candidate given by PepQuery
• PepQuery_mods: Modifications in the peptide candidate given by PepQuery
• PepQueryPTM_sequence: Canonical peptide candidate including rare modifications given by PepQuery
• PepQueryPTM_mods: List of modifications in the peptide candidate including rare modifications given by PepQuery
• PepQuery_variant_score: PepQuery score for the variant match
• PepQuery_ref_score: PepQuery score for the canonical match
• PepQuery_PTM_score: PepQuery score for the matching peptide including rare modifications

References

[1] Spooner, W., McLaren, W., Slidel, T., Finch, D.K., Butler, R., Campbell, J., Eghobamien, L., Rider, D., Kiefer, C.M., Robinson, M.J., et al. (2018) Haplosaurus computes protein haplotypes for use in precision drug design. Nat. Commun., 9, 4128.