Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF.

Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence within human leukocyte antigen (HLA) class-specific length restrictions needs to be considered during sequence database searching. This leads to an inflation of the search space and results in lower spectrum annotation rates. Peptide-spectrum match (PSM) rescoring is a powerful enhancement of standard searching that boosts the spectrum annotation performance. We analyze 302,105 unique synthesized non-tryptic peptides from the ProteomeTools project on a timsTOF-Pro to generate a ground-truth dataset containing 93,227 MS/MS spectra of 74,847 unique peptides, that is used to fine-tune the deep learning-based fragment ion intensity prediction model Prosit. We demonstrate up to 3-fold improvement in the identification of immunopeptides, as well as increased detection of immunopeptides from low input samples.

Deep Learning-Assisted Analysis of Immunopeptidomics Data.

Liquid chromatography-coupled mass spectrometry (LC-MS/MS) is the primary method to obtain direct evidence for the presentation of disease- or patient-specific human leukocyte antigen (HLA). However, compared to the analysis of tryptic peptides in proteomics, the analysis of HLA peptides still poses computational and statistical challenges. Recently, fragment ion intensity-based matching scores assessing the similarity between predicted and observed spectra were shown to substantially increase the number of confidently identified peptides, particularly in use cases where non-tryptic peptides are analyzed. In this chapter, we describe in detail three procedures on how to benefit from state-of-the-art deep learning models to analyze and validate single spectra, single measurements, and multiple measurements in mass spectrometry-based immunopeptidomics. For this, we explain how to use the Universal Spectrum Explorer (USE), online Oktoberfest, and offline Oktoberfest. For intensity-based scoring, Oktoberfest uses fragment ion intensity and retention time predictions from the deep learning framework Prosit, a deep neural network trained on a very large number of synthetic peptides and tandem mass spectra generated within the ProteomeTools project. The examples shown highlight how deep learning-assisted analysis can increase the number of identified HLA peptides, facilitate the discovery of confidently identified neo-epitopes, or provide assistance in the assessment of the presence of cryptic peptides, such as spliced peptides.

Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit.

Machine learning (ML) and deep learning (DL) models for peptide property prediction such as Prosit have enabled the creation of high quality in silico reference libraries. These libraries are used in various applications, ranging from data-independent acquisition (DIA) data analysis to data-driven rescoring of search engine results. Here, we present Oktoberfest, an open source Python package of our spectral library generation and rescoring pipeline originally only available online via ProteomicsDB. Oktoberfest is largely search engine agnostic and provides access to online peptide property predictions, promoting the adoption of state-of-the-art ML/DL models in proteomics analysis pipelines. We demonstrate its ability to reproduce and even improve our results from previously published rescoring analyses on two distinct use cases. Oktoberfest is freely available on GitHub (https://github.com/wilhelm-lab/oktoberfest) and can easily be installed locally through the cross-platform PyPI Python package.

Network medicine-based epistasis detection in complex diseases: ready for quantum computing.

Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover the clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs)1-3. Existing statistical computational methods for EI detection are mostly limited to pairs of SNPs due to the combinatorial explosion of higher-order EIs. With NeEDL (network-based epistasis detection via local search), we leverage network medicine to inform the selection of EIs that are an order of magnitude more statistically significant compared to existing tools and consist, on average, of five SNPs. We further show that this computationally demanding task can be substantially accelerated once quantum computing hardware becomes available. We apply NeEDL to eight different diseases and discover genes (affected by EIs of SNPs) that are partly known to affect the disease, additionally, these results are reproducible across independent cohorts. EIs for these eight diseases can be interactively explored in the Epistasis Disease Atlas (https://epistasis-disease-atlas.com). In summary, NeEDL is the first application that demonstrates the potential of seamlessly integrated quantum computing techniques to accelerate biomedical research. Our network medicine approach detects higher-order EIs with unprecedented statistical and biological evidence, yielding unique insights into polygenic diseases and providing a basis for the development of improved risk scores and combination therapies.