Variant Peptide Identification

Code related to the "Retention time and fragmentation predictors increase confidence in variant peptide identification" publication: ...

Requirements and Usage

Required software to reproduce the figures in the paper are Snakemake and conda, other required python libraries are specified at diagnostic_plots_env.yaml and the corresponding environment is automatically created by Snakemake.

• Download supplementary data from: https://doi.org/10.6084/m9.figshare.22354666.v1

• Clone this repository

• Adjust the paths to the data in Snakefile if necessary

• Create diagnostic plots by executing snakemake --cores <# cores> --use-conda

Supplementary data

The supplementary data include the PSM and peptide level exports obtained from the analysis presented in this paper. A proteomic dataset (provided by Wang et al. [1]) with MS/MS spectra from 3 samples was searched against 4 human protein databases (see publication for details):

• UniProt canonical proteome (UniProt)

• UniProt including isoforms (UniProt_isoforms)

• Ensembl including isoforms (Ensembl_reference)

• Ensembl including isoforms and products of common genetic variants (extendedDB)

The exports contain a line per PSM/peptide with all relevant identifiers, features used for statistical evaluation, and confidence metrics.
More detailed description of the columns of the exports are available at exports_documentation.txt and Table 2 and 3 of the publication.

The 4 used protein sequence databases are also included in the suppementary data.

References

[1] D. Wang, B. Eraslan, T. Wieland, B. Hallström, T. Hopf, D. P. Zolg, J. Zecha, A. Asplund, L.-h. Li, C. Meng, M. Frejno, T. Schmidt, K. Schnatbaum, M. Wilhelm, F. Ponten, M. Uhlen, J. Gagneur, H. Hahne, and B. Kuster, “A deep proteome and transcriptome abundance atlas of 29 healthy human tissues,” Molecular Systems Biology, vol. 15, no. 2, p. e8503, 2019.