Development of Data-Independent Acquisition-mass spectrometry strategy for immunopeptidomics analysis

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TMUIR > College of Pharmacy > Master Program for Clinical Pharmacogenomics and Pharmacoproteomics > Dissertations/Theses > Item 987654321/62401

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Title:	Development of Data-Independent Acquisition-mass spectrometry strategy for immunopeptidomics analysis Development of Data-Independent Acquisition-mass spectrometry strategy for immunopeptidomics analysis
Authors:	HOA, VO THANH
Contributors:	臨床基因體學暨蛋白質體學碩士學位學程 Chia-Li Han
Keywords:	Data-independent-acquisition;mass spectrometry;proteogenomics;neoantigen;human leukocyte antigen
Date:	2022-07-07
Issue Date:	2022-12-29 11:09:21 (UTC+8)
Abstract:	Antigen presentation by the human leukocyte antigen proteins plays a critical role in the regulation of the immune system to trigger antitumor response in cancer. By targeting neoantigens, tumor destruction via anticancer T-cell responses will be achieved without causing damage to normal tissues. Data-independent-acquisition mass spectrometry (DIA-MS) emerges as an effective method for detecting low-abundance proteins by collecting fragment ion spectra regardless of precursor ion intensities, which subsequently facilitates the detection of neoantigen. However, the application of DIA-MS in neoantigen detection is challenging because of the limited spectral library, resulting in few identifications. Therefore, the aim of our study is to optimize the DIA-MS platform to leverage HLA-binding peptides and potential neoantigen identification. Two lung cancer cell lines, H1975 cells and CRISPR9-edited H1975 cells with additional EGFR C797S mutation are our study model. Firstly, we expanded the experimental peptide spectral library to a total of 4,746 peptides by including the spectra identified from the reported mono-HLA allelic cell lines and our immunoprecipitation experiments. Secondly, we constructed a virtual spectral library that combines the predicted spectra of putative 23,404 mutant and 542,444 wild-type peptides. Third, we generated a hybrid spectral library by integrating the experimental and virtual libraries to aid the identification of 570 HLA-binding peptides and 102 mutant peptides in both cells. Further functional analysis of the mutant peptides suggested FVLEDPTLL peptide derived from I83V mutation of Adenylate Cyclase 2 as a potential neoantigen in lung cancer. We expect that this DIA-MS platform will be a powerful tool for enhancing neoantigen discovery and fostering personalized treatment upon clinical application.
Description:	碩士指導教授：Chia-Li Han 委員：Chia-Li Han 委員：San-Yuan Wang 委員：I-Lin Tsai
Data Type:	thesis
Appears in Collections:	[Master Program for Clinical Pharmacogenomics and Pharmacoproteomics] Dissertations/Theses

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