Journal Article

Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data

Degenhardt, Frauke, Bacher, Petra, Wendorff, Mareike, ElAbd, Hesham, Tholey, Andreas, Franke, Andre, Kamps, Ann-Kristin, Koudelka, Tomas, Lenz, Tobias L.

2021

Overview

Background The human leukocyte antigen (HLA) proteins play a fundamental role in the adaptive immune system as they present peptides to T cells. Mass-spectrometry-based immunopeptidomics is a promising and powerful tool for characterizing the immunopeptidomic landscape of HLA proteins, that is the peptides presented on HLA proteins. Despite the growing interest in the technology, and the recent rise of immunopeptidomics-specific identification pipelines, there is still a gap in data-analysis and software tools that are specialized in analyzing and visualizing immunopeptidomics data. Results We present the IPTK library which is an open-source Python-based library for analyzing, visualizing, comparing, and integrating different omics layers with the identified peptides for an in-depth characterization of the immunopeptidome. Using different datasets, we illustrate the ability of the library to enrich the result of the identified peptidomes. Also, we demonstrate the utility of the library in developing other software and tools by developing an easy-to-use dashboard that can be used for the interactive analysis of the results. Conclusion IPTK provides a modular and extendable framework for analyzing and integrating immunopeptidomes with different omics layers. The library is deployed into PyPI at https://pypi.org/project/IPTKL/ and into Bioconda at https://anaconda.org/bioconda/iptkl , while the source code of the library and the dashboard, along with the online tutorials are available at https://github.com/ikmb/iptoolkit .

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Adaptive systems / Algorithms / Analysis / Antigen processing and presentation / Antigens / Bioinformatics / Biomedical and Life Sciences / Computational Biology/Bioinformatics / Computational immunology / Computer Appl. in Life Sciences / Computer programs / Dashboards / Data analysis / Data processing / Experiments / Gene expression / Histocompatibility antigen HLA / Histocompatibility antigens / HLA / HLA histocompatibility antigens / Identification / Immune system / Immunopeptidomics / Information management / Interactive data analysis / Leukocytes / Libraries / Life Sciences / Lymphocytes / Lymphocytes T / Methods / Microarrays / Online tutorials / Peptides / Pipelines / Proteins / Proteomics / Scientific imaging / Software / Software development tools / Source code / Spectrometry / Toolkits / Visualization