Online spectrum identification validation by comparison to predicted/experimental spectra

[tkschmidt]

Abstract

Confirmation of a single MS2 spectrum identification by comparison to other spectra is still not simple (enough). Although many different resources like PRMAtlas, MassIVE and ProteomicsDB have a deep back catalog of high-confidence mass spectra, they are not easily obtainable. ProteomicsDB wants to change this now and will extend its API following the FAIR principles (FAIR data meets standards of findability, accessibility, interoperability, and reusability). This offers a direct and query-able interface to >108,000,000 experimental spectra covering >70% of the human and arabidopsis proteome. Every experimental spectrum comes with detailed meta-data of the underlying experimental and acquisition schema. Additionally, virtually any (unmodified) peptide can be predicted in high quality by the deep-learning algorithm Prosit and can also be accessed via the above-mentioned API.
We want to combine this REST interface with the core visualizations of the Interactive Peptide Spectral Annotator (IPSA) to build a minimal website for researchers to visualize their acquired spectra and get an instantaneous comparison to an external source.
By designing a common interface for requesting and receiving spectral data from any online resource, we hope to encourage other resources like MassIVE, as well as other prediction tools like MS2PIP to join this effort.

Work plan

First, we will give a short introduction to how the API of ProtemicsDB is setup. Secondly, we will try to figure out different ways to show multiple spectra and how this fits best with the existing codebase. Additionally, we will discuss which measures can be used to objectively judge an agreement between the uploaded spectrum and the provided ones, and what their pros and cons are.
Then, we will explore how to extend IPSA, create a minimal website for easier development and cycle through the gathered ideas.

Technical details

The core visualization feature of the IPSA is developed in the JavaScript library D3.js which will allow us rapid prototyping of the additional features. The API of ProteomicsDB will provide the spectrum information in various formats e.g. JSON or XML.

Contact information

Mathias Wilhelm - TU Muenchen (Germany) - mathias.wilhelm@tum.de
Tobias Schmidt – TU Muenchen (Germany) - tobias.k.schmidt@tum.de
Patroklos Smaras – TU Muenchen (Germany) - patroklos.samaras@tum.de