Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins
Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins
复制标题
DOI：
10.1038/sdata.2019.11
复制
发表时间：
2019-02-12
期刊：
影响因子：
9.8
通讯作者：
Aebersold, Ruedi
中科院分区：
文献类型：
--
作者：
Blattmann, Peter;Stutz, Vivienne;Aebersold, Ruedi
所有理论质谱的连续窗口采集（SWATH-MS）需要一个光谱库，以便从数据独立采集模式（DIA）下采集的质谱数据中提取定量测量值。包含SWATH测定的大型组合光谱库已经为人类和其他几种生物体产生，但到目前为止，还没有公开可用的库用于测量斑马鱼的蛋白质组，这是生物医学研究中迅速出现的模型系统。在这里，我们提出了一个大型的斑马鱼SWATH光谱库来测量10,405个蛋白质中104,185个蛋白质型肽的丰度。该文库包括在9种不同的斑马鱼组织（脑、眼、心脏、肠、肝脏、肌肉、卵巢、脾脏和睾丸）中表达的蛋白质，并提供了一个重要的新资源来量化40%的编码蛋白质的斑马鱼基因。我们利用这一资源来量化大脑，肌肉和肝脏的蛋白质组，并表征不同组织中旁系同源蛋白质的不同表达水平。数据可通过ProteomeXchange（PXD 010876、PXD 010869）和SWATHAtlas（PASS 01237）获得。
Sequential window acquisition of all theoretical mass spectra (SWATH-MS) requires a spectral library to extract quantitative measurements from the mass spectrometry data acquired in data-independent acquisition mode (DIA). Large combined spectral libraries containing SWATH assays have been generated for humans and several other organisms, but so far no publicly available library exists for measuring the proteome of zebrafish, a rapidly emerging model system in biomedical research. Here, we present a large zebrafish SWATH spectral library to measure the abundance of 104,185 proteotypic peptides from 10,405 proteins. The library includes proteins expressed in 9 different zebrafish tissues (brain, eye, heart, intestine, liver, muscle, ovary, spleen, and testis) and provides an important new resource to quantify 40% of the protein-coding zebrafish genes. We employ this resource to quantify the proteome across brain, muscle, and liver and characterize divergent expression levels of paralogous proteins in different tissues. Data are available via ProteomeXchange (PXD010876, PXD010869) and SWATHAtlas (PASS01237).