2018,
Scientific Data.
DOI:
10.1038/sdata.2018.157
A tissue-based draft map of the murine MHC class I immunopeptidome
Heiko Schuster
, Wenguang Shao
, Tobias Weiss
, Patrick G.A. Pedrioli
, Patrick Roth
, Michael Weller
, David S. Campbell
, Eric W. Deutsch
, Robert L. Moritz
, Oliver Planz
, Hans-Georg Rammensee
, Ruedi Aebersold
, Etienne Caron
Abstract:
Abstract The large array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC class I immunopeptidome. Although the MHC class I immunopeptidome is ubiquitous in mammals and represents a critical component of the immune system, very little is known, in any species, about its composition across most tissues and organs in vivo . We applied mass spectrometry (MS) technologies to draft the first tissue-based atlas of the murine MHC class I immunopeptidome in health. Peptides were extracted from 19 normal tissues from C57BL/6 mice and prepared for MS injections, resulting in a total number of 28,448 high-confidence H2Db /Kb -associated peptides identified and annotated in the atlas. This atlas provides initial qualitative data to explore the tissue-specificity of the immunopeptidome and serves as a guide to identify potential tumor-associated antigens from various cancer models. Our data were shared via PRIDE (PXD008733), SysteMHC Atlas (SYSMHC00018) and SWATH Atlas. We anticipate that this unique dataset will be expanded in the future and will find wide applications in basic and translational immunology.
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2023-09-01 00:00:30
小年:
#paper https://doi.org/10.1038/sdata.2018.157 A tissue-based draft map of the murine MHC class I immunopeptidome 文章介绍了一个关于小鼠MHC I类免疫肽组的组织图谱，其中包含了19种正常组织中呈现给CD8+ T细胞的肽段的全面概述。方法总结如下：
1. 得到质谱下机数据。
2. 使用Msconvert将原始质谱数据转换为mzML格式。
3. 使用Comet、MS-GF+和XTandem等数据库搜索引擎，将mzML格式的数据与小鼠蛋白质数据库进行比对，以鉴定肽段。
4. 使用Prophets进行统计验证，以确定鉴定的肽段的置信度。
5. 使用GibbsCluster v.1对鉴定的肽段进行聚类分析，以确定具有相似质谱特征的肽段。
6. 使用NetMHC v.4对鉴定的肽段进行注释分析，以确定其长度和预测MHC结合亲和力。
7. 根据统计验证和注释分析的结果，筛选出高置信度的MHC相关肽段。
8. 使用高置信度的MHC相关肽段，构建高质量的H2D b/K b特异性肽段光谱和测定库。
9. 将构建的肽段光谱和测定库共享到SysteMHC Atlas和SWATH Atlas中，以便其他研究人员可以使用和分析这些数据。
10. 最终的结果呈现，包括肽段光谱和测定库的构建、MHC相关肽段的注释和筛选等。