Dataset Information

DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics.

ABSTRACT: The identification of major histocompatibility complex (MHC)-binding peptides in mass spectrometry (MS)-based immunopeptideomics relies largely on database search engines developed for proteomics data analysis. However, because immunopeptidomics experiments do not involve enzymatic digestion at specific residues, an inflated search space leads to a high false positive rate and low sensitivity in peptide identification. In order to improve the sensitivity and reliability of peptide identification, a post-processing tool named DeepRescore is developed. DeepRescore combines peptide features derived from deep learning predictions, namely accurate retention timeand MS/MS spectra predictions, with previously used features to rescore peptide-spectrum matches. Using two public immunopeptidomics datasets, it is shown that rescoring by DeepRescore increases both the sensitivity and reliability of MHC-binding peptide and neoantigen identifications compared to existing methods. It is also shown that the performance improvement is, to a large extent, driven by the deep learning-derived features. DeepRescore is developed using NextFlow and Docker and is available at https://github.com/bzhanglab/DeepRescore.

SUBMITTER: Li K

PROVIDER: S-EPMC7718998 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics.

Li Kai K Jain Antrix A Malovannaya Anna A Wen Bo B Zhang Bing B

Proteomics 20200927 21-22

The identification of major histocompatibility complex (MHC)-binding peptides in mass spectrometry (MS)-based immunopeptideomics relies largely on database search engines developed for proteomics data analysis. However, because immunopeptidomics experiments do not involve enzymatic digestion at specific residues, an inflated search space leads to a high false positive rate and low sensitivity in peptide identification. In order to improve the sensitivity and reliability of peptide identification ...[more]

PMID: 32864883

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Project description:Antimicrobial peptides (AMPs) are excellent at fighting many different infections. This demonstrates how important it is to make new AMPs that are even better at eliminating infections. The fundamental transformation in a variety of scientific disciplines, which led to the emergence of machine learning techniques, has presented significant opportunities for the development of antimicrobial peptides. Machine learning and deep learning are used to predict antimicrobial peptide efficacy in the study. The main purpose is to overcome traditional experimental method constraints. Gram-negative bacterium Escherichia coli is the model organism in this study. The investigation assesses 1,360 peptide sequences that exhibit anti- E. coli activity. These peptides' minimal inhibitory concentrations have been observed to be correlated with a set of 34 physicochemical characteristics. Two distinct methodologies are implemented. The initial method involves utilizing the pre-computed physicochemical attributes of peptides as the fundamental input data for a machine-learning classification approach. In the second method, these fundamental peptide features are converted into signal images, which are then transmitted to a deep learning neural network. The first and second methods have accuracy of 74% and 92.9%, respectively. The proposed methods were developed to target a single microorganism (gram negative E.coli), however, they offered a framework that could potentially be adapted for other types of antimicrobial, antiviral, and anticancer peptides with further validation. Furthermore, they have the potential to result in significant time and cost reductions, as well as the development of innovative AMP-based treatments. This research contributes to the advancement of deep learning-based AMP drug discovery methodologies by generating potent peptides for drug development and application. This discovery has significant implications for the processing of biological data and the computation of pharmacology.

Dataset Information

DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics.

Publications

DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics.

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