PMID- 34404349
OWN - NLM
STAT- MEDLINE
DCOM- 20210819
LR  - 20210821
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 22
IP  - 1
DP  - 2021 Aug 17
TI  - Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for 
      analyzing immunopeptidomics data.
PG  - 405
LID - 10.1186/s12859-021-04315-0 [doi]
LID - 405
AB  - 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 .
CI  - (c) 2021. The Author(s).
FAU - ElAbd, Hesham
AU  - ElAbd H
AD  - Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 
      Kiel, Germany.
FAU - Degenhardt, Frauke
AU  - Degenhardt F
AD  - Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 
      Kiel, Germany.
FAU - Koudelka, Tomas
AU  - Koudelka T
AD  - Proteomics and Bioanalytics, Institute for Experimental Medicine, 
      Christian-Albrechts-University of Kiel, Kiel, Germany.
FAU - Kamps, Ann-Kristin
AU  - Kamps AK
AD  - Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 
      Kiel, Germany.
AD  - Institute of Immunology, Christian-Albrechts-University of Kiel, Kiel, Germany.
FAU - Tholey, Andreas
AU  - Tholey A
AD  - Proteomics and Bioanalytics, Institute for Experimental Medicine, 
      Christian-Albrechts-University of Kiel, Kiel, Germany.
FAU - Bacher, Petra
AU  - Bacher P
AD  - Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 
      Kiel, Germany.
AD  - Institute of Immunology, Christian-Albrechts-University of Kiel, Kiel, Germany.
FAU - Lenz, Tobias L
AU  - Lenz TL
AD  - Research Unit for Evolutionary Immunogenomics, Department of Biology, University 
      of Hamburg, Hamburg, Germany.
FAU - Franke, Andre
AU  - Franke A
AUID- ORCID: 0000-0003-1530-5811
AD  - Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 
      Kiel, Germany. a.franke@mucosa.de.
FAU - Wendorff, Mareike
AU  - Wendorff M
AD  - Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 
      Kiel, Germany.
LA  - eng
GR  - Research Training Group 1743, 'Genes, Environment and Inflammation'/Deutsche 
      Forschungsgemeinschaft (DE)/
GR  - Research Training Group 1743, 'Genes, Environment and Inflammation'/Deutsche 
      Forschungsgemeinschaft/
GR  - EXC 2167-390884018/Deutsche Forschungsgemeinschaft/
PT  - Journal Article
DEP - 20210817
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptides)
SB  - IM
MH  - *Data Analysis
MH  - Histocompatibility Antigens Class I
MH  - Humans
MH  - Mass Spectrometry
MH  - Peptides
MH  - *Software
PMC - PMC8369717
OTO - NOTNLM
OT  - Antigen processing and presentation
OT  - Computational immunology
OT  - HLA
OT  - Immunopeptidomics
OT  - Interactive data analysis
COIS- The authors declare that they have no competing interests.
EDAT- 2021/08/19 06:00
MHDA- 2021/08/20 06:00
PMCR- 2021/08/17
CRDT- 2021/08/18 05:33
PHST- 2021/01/20 00:00 [received]
PHST- 2021/08/03 00:00 [accepted]
PHST- 2021/08/18 05:33 [entrez]
PHST- 2021/08/19 06:00 [pubmed]
PHST- 2021/08/20 06:00 [medline]
PHST- 2021/08/17 00:00 [pmc-release]
AID - 10.1186/s12859-021-04315-0 [pii]
AID - 4315 [pii]
AID - 10.1186/s12859-021-04315-0 [doi]
PST - epublish
SO  - BMC Bioinformatics. 2021 Aug 17;22(1):405. doi: 10.1186/s12859-021-04315-0.