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# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  PTMVision: An Interactive Visualization Webserver for
  Post-translational Modifications of Proteins
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Simon
    family-names: Hackl
    orcid: "https://orcid.org/0009-0000-3596-3411"
  - given-names: Caroline
    family-names: Jachmann
    orcid: "https://orcid.org/0009-0000-4679-7295"
  - given-names: Mathias
    family-names: Witte Paz
    orcid: "https://orcid.org/0000-0001-8113-4139"
  - given-names: Theresa Anisja
    family-names: Harbig
    orcid: "https://orcid.org/0000-0001-8716-5788"
  - given-names: Lennart
    family-names: Martens
    orcid: "https://orcid.org/0000-0003-4277-658X"
  - given-names: Kay
    family-names: Nieselt
    orcid: "https://orcid.org/0000-0002-1283-7065"
identifiers:
  - type: doi
    value: 10.1021/acs.jproteome.4c00679
    description: Article
  - type: other
    value: "39772617"
    description: PMID
repository-code: "https://github.com/Integrative-Transcriptomics/PTMVision"
url: "https://ptmvision-tuevis.cs.uni-tuebingen.de/"
repository: "https://doi.org/10.5281/zenodo.13270568"
abstract: >-
  Recent improvements in methods and instruments used in
  mass spectrometry have greatly enhanced the detection of
  protein post-translational modifications (PTMs). On the
  computational side, the adoption of open modification
  search strategies now allows for the identification of a
  wide variety of PTMs, potentially revealing hundreds to
  thousands of distinct modifications in biological samples.
  While the observable part of the proteome is continuously
  growing, the visualization and interpretation of this vast
  amount of data in a comprehensive fashion is not yet
  possible. There is a clear need for methods to easily
  investigate the PTM landscape and to thoroughly examine
  modifications on proteins of interest from acquired mass
  spectrometry data. We present PTMVision, a web server
  providing an intuitive and simple way to interactively
  explore PTMs identified in mass spectrometry-based
  proteomics experiments and to analyze the modification
  sites of proteins within relevant context. It offers a
  variety of tools to visualize the PTM landscape from
  different angles and at different levels, such as 3D
  structures and contact maps, UniMod classification
  summaries, and site specific overviews. The web server’s
  user-friendly interface ensures accessibility across
  diverse scientific backgrounds.
keywords:
  - post-translational modifications
  - open search
  - visualization
  - Web server
license: GPL-3.0
commit: 117dfdfea1a600f374e4bc85bef02dd57959920a
version: "2.0"
date-released: "2025-01-08"
preferred-citation:
  type: article
  authors:
    - given-names: Simon
      family-names: Hackl
      orcid: "https://orcid.org/0009-0000-3596-3411"
    - given-names: Caroline
      family-names: Jachmann
      orcid: "https://orcid.org/0009-0000-4679-7295"
    - given-names: Mathias
      family-names: Witte Paz
      orcid: "https://orcid.org/0000-0001-8113-4139"
    - given-names: Theresa Anisja
      family-names: Harbig
      orcid: "https://orcid.org/0000-0001-8716-5788"
    - given-names: Lennart
      family-names: Martens
      orcid: "https://orcid.org/0000-0003-4277-658X"
    - given-names: Kay
      family-names: Nieselt
      orcid: "https://orcid.org/0000-0002-1283-7065"
  doi: "10.1021/acs.jproteome.4c00679"
  journal: "Journal of Proteome Research"
  start: 919 # First page number
  end: 928 # Last page number
  title: "PTMVision: An Interactive Visualization Webserver for Post-translational Modifications of Proteins"
  volume: 24
  number: 2
  year: 2025
  note: "PMID: 39772617"
  URL: "https://doi.org/10.1021/acs.jproteome.4c00679"
  eprint: "https://doi.org/10.1021/acs.jproteome.4c00679"