Explainable Machine Learning for Identifying the Full Heterogeneity of Peptidoforms and Proteoforms

Introduction

Mass spectrometry driven proteomics allows deep insights into the working of cells. Still, the vast majority of proteoforms, representing the full heterogeneity of molecular forms of protein products in a sample, currently remain undetected in proteomics experiments.

Knowledge Gaps

This lack of information strongly restricts our knowledge of disease progression, possible biomarkers, and therapeutic targets across a large number of diseases. Several machine learning approaches have been developed for proteomics data, but not being trained end-to-end, they cannot capture the full wealth of proteomic mass spectra and commonly remain unexplained black boxes.

Project Overview

Within explAInProt, my team and I will develop representations of spectra that allow deploying explainable, end-to-end machine learning models on the wealth of proteomic data available, regarding both bottom-up and top-down spectra to identify novel protein variants.

Importance of Explanations

Explanations will allow identifying the origin of predictions and will help reduce bias, building up the trustworthiness of AI systems required for clinical applications.

Verification Strategies

To verify results, we will pioneer orthogonal real-time strategies based on selective sequencing approaches and calling of amino acids that we will introduce for nanopore sequencing devices as a complementary acquisition method.

Addressing Dark Matter

All combined, this will allow us to drastically increase our knowledge about the current dark matter of mass spectrometry driven proteomics: those proteins and peptides that are non-canonically modified, non-tryptic, have potentially multiple amino acid substitutions, or no close match in databases, or result from structural variants such as fusion proteins that remain undetected in current analyses.

Applicability

We will highlight applicability in two areas of particular concern in current approaches:

1. The detection of structural variants in proteomic mass spectra.
2. The characterization of novel microbial organisms without sufficient database information.