PTMVision: Interactive Visualization of Post Translational Modifications

Example of the Site Count Histogram.

PTMVision supports the upload of PTM data from various proteomics search engines, the mzIdentML standard or manually compiled CSV files.

Example of the Site Count Histogram.

Receive a quantitative and qualitative assessment of the PTMs in your data, independent of individual proteins. Get an overview of all available proteins from your data, complemented with associated PTMs.

Example of the Site Count Histogram.

For selected proteins, investigate detailed information on the occurrence of PTMs along the primary protein sequence and in a spatial structural context.

About PTMVision

Understanding the intricate landscape of PTMs is crucial for unraveling the complex mechanisms underlying cellular processes and diseases. PTMVision (Interactive Visualization of Post Translational Modifications) is an interactive web platform for effortless exploratory visual analysis of post translational modifications (PTMs) obtained from mass spectrometry (MS) data using search engines such as ionbot, MaxQuant, MSFragger, Spectronaut, or Sage. The application is designed in close collaboration with proteomics experts and was initiated as an entry to the Bio+MedVis Challenge at the IEEE VIS conference in 2022. PTMVision is accessible to laboratory researchers without requiring coding skills.

Key Features
  • Variety of overview and summary visualizations that help identify patterns and trends in PTM data.
  • Visualizations are dynamically linked and support features to highlight PTMs of interest.
  • Integration of protein structure and annotation data from UniProt provide multidimensional view. This improves the interpretability of the data significantly.
  • Unique emphasis on interactions of residues in close contact within a single protein and associated modifications. This allows to study the dynamic interplay between PTMs and their putative effects on protein folding and function.
  • Responsive and intuitive interface that allows users to effortlessly navigate the website and through their data.
  • Supports high degree of data provenance by allowing various input formats and an easy export of session data to continue analysis without repeated processing input data.
Limitations
  • We recommend using PTMVision in Chrome or Firefox for optimal performance. Safari has issues when visualising larger datasets.
  • Note that PTMVision serves solely to visualize the content provided in the input and does not conduct any further quality control. The localization of modifications still remains a challenging task and may yield imprecise results.
  • PTMVision will be continuously updated and improved, including the addition of filters for localisation scores as soon as they will be reported by search engines.
  • PTMVision currently limits the maximal request size with respect to the zlib compressed content of the PTM Data file to a maximum of 50 MB.
Start Session

Upload data, re-upload a session or browse and start an example session. Once complete, session data can be downloaded with Download Session Data in the header menu and panels and will be filled. Click symbols for help.

PTMVision sessions are stored for 24 hours on our server and will be deleted afterwards (existing session data is automatically re-initialized).

Upload post-translational modification data from open or closed search to start a new session

Mandatory Input Format

Mandatory PTM Data

Optional Exclude UniMod Classes

Optional Adjust Mass Shift Tolerance


or re-upload a PTMVision session

Mandatory PTMVision Session

or

Overview PTMs
Select Single Protein of Interest

Overview of all proteins available from session data, listing one protein per row with basic information about the protein and associated PTMs. Select a single row by clicking on it (highlighted in red) and click Display to obtain a detailed view of the PTMs on the selected protein. Click symbols for help.

Filter for modifications by UniMod name

Filter for protein names/UniProt identifier

ID
Name
Primary Sequence Length
No. modified positions
No. distinct modifications

Explore Detail No Protein Selected