MHCquant2 refines immunopeptidomics tumor antigen discovery

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Jonas Scheid, Steffen Lemke, Naomi Hoenisch-Gravel, Anna Dengler, Timo Sachsenberg, Arthur Declerq, Ralf Gabriels, Jens Bauer, Marcel Wacker, Leon Bichmann, Lennart Martens, Marissa L. Dubbelaar, Sven Nahnsen, Juliane S. Walz
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引用次数: 0

Abstract

Confident identification of human leukocyte antigen (HLA)-presented peptides is crucial for advancing cancer immunotherapy. We present MHCquant2, a scalable and modular Nextflow pipeline integrated into nf-core as a reproducible, portable, and standardized workflow for immunopeptidomics. This integration allows a community-driven, robust solution for high-throughput analyses across operating systems and cloud infrastructures. MHCquant2 integrates open-source tools including OpenMS, DeepLC, and MS2PIP, improving peptide identifications by up to 27% across diverse MS platforms, particularly enriching low-abundant peptides. MHCquant2 demonstrates state-of-the-art performance on our novel benignMHCquant2 dataset (n = 92) and expands the benign human immunopeptidome by over 160,000 unique naturally presented HLA peptides.
MHCquant2改进免疫肽组学肿瘤抗原发现
人类白细胞抗原(HLA)呈递肽的自信鉴定对于推进癌症免疫治疗至关重要。我们提出MHCquant2,一个可扩展和模块化的Nextflow管道集成到nf-core中,作为免疫肽组学的可复制,便携式和标准化工作流程。这种集成为跨操作系统和云基础设施的高吞吐量分析提供了社区驱动的健壮解决方案。MHCquant2集成了开源工具,包括OpenMS, DeepLC和MS2PIP,在不同的MS平台上提高了高达27%的肽鉴定,特别是富集低丰度的肽。MHCquant2在我们的新型良性MHCquant2数据集(n = 92)上展示了最先进的性能,并通过超过160,000种独特的自然呈现的HLA肽扩展了良性人类免疫肽穹窿。
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来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
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