Braccia Clarissa, Espinal Meritxell Pons, Pini Mattia, De Pietri Tonelli Davide, Armirotti Andrea
D3 PharmaChemistry, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
Neurobiology of miRNA Lab, Neuroscience and Brain Technologies Department, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
Data Brief. 2018 Feb 27;18:1-8. doi: 10.1016/j.dib.2018.02.062. eCollection 2018 Jun.
Over the last years, the SWATH data-independent acquisition protocol (Sequential Window acquisition of All THeoretical mass spectra) has become a cornerstone for the worldwide proteomics community (Collins et al., 2017) [1]. In this approach, a high-resolution quadrupole-ToF mass spectrometer acquires thousands of MS/MS data by selecting not just a single precursor at a time, but by allowing a broad / range to be fragmented. This acquisition window is then sequentially moved from the lowest to the highest mass selection range. This technique enables the acquisition of thousands of high-resolution MS/MS spectra per minute in a standard LC-MS run. In the subsequent data analysis phase, the corresponding dataset is searched in a "triple quadrupole-like" mode, thus not considering the whole MS/MS scan spectrum, but by searching for several precursor to fragment transitions that identify and quantify the corresponding peptide. This search is made possible with the use of an ion library, previously acquired in a classical data dependent, full-spectrum mode (Fabre et al., 2017; Wu et al., 2017) [2], [3]. The SWATH protocol, combining the protein identification power of high-resolution MS/MS spectra with the robustness and accuracy in analyte quantification of triple-quad targeted workflows, has become very popular in proteomics research. The major drawback lies in the ion library itself, which is normally demanding and time-consuming to build. Conversely, through the realignment of chromatographic retention times, an ion library of a given proteome can relatively easily be tailored upon "any" proteomics experiment done on the same proteome. We are thus hereby sharing with the worldwide proteomics community our newly acquired ion library of mouse adult hippocampal neural stem cells. Given the growing effort in neuroscience research involving proteomics experiments (Pons-Espinal et al., 2017; Sarnyai and Guest, 2017; Sethi et al., 2015; Bramini et al., 2016) [4,[5], [6], [7], we believe that this data might be of great help for the neuroscience community. All the here reported data (RAW files, results and ion library) can be freely downloaded from the SWATHATLAS (Deutsch et al., 2008) [8] website (http://www.peptideatlas.org/PASS/PASS01110).
在过去几年中，SWATH数据非依赖型采集协议（全理论质谱图的顺序窗口采集）已成为全球蛋白质组学领域的基石（Collins等人，2017年）[1]。在这种方法中，高分辨率四极杆-飞行时间质谱仪通过一次不仅选择单个前体，而且允许一个宽质量范围被碎裂来获取数千个MS/MS数据。然后，这个采集窗口从最低质量选择范围依次移动到最高质量选择范围。该技术能够在标准液相色谱-质谱分析中每分钟获取数千个高分辨率MS/MS谱图。在随后的数据分析阶段，相应的数据集以“类似三重四极杆”的模式进行搜索，因此不是考虑整个MS/MS扫描谱图，而是通过搜索几个用于鉴定和定量相应肽段的前体到碎片的跃迁。利用先前在经典的数据依赖型全谱模式下获取的离子库（Fabre等人，2017年；Wu等人，2017年）[2]，[3]，使得这种搜索成为可能。SWATH协议将高分辨率MS/MS谱图的蛋白质鉴定能力与三重四极杆靶向工作流程中分析物定量的稳健性和准确性相结合，在蛋白质组学研究中变得非常流行。主要缺点在于离子库本身，其构建通常要求高且耗时。相反，通过重新校准色谱保留时间，给定蛋白质组的离子库可以相对容易地根据在同一蛋白质组上进行的“任何”蛋白质组学实验进行定制。因此，我们在此与全球蛋白质组学领域分享我们新获得的小鼠成年海马神经干细胞离子库。鉴于涉及蛋白质组学实验的神经科学研究工作日益增加（Pons-Espinal等人，2017年；Sarnyai和Guest，2017年；Sethi等人，2015年；Bramini等人，2016年）[4，[5]，[6]，[7]，我们相信这些数据可能对神经科学领域有很大帮助。所有在此报告的数据（原始文件、结果和离子库）均可从SWATHATLAS（Deutsch等人，2008年）[8]网站（http://www.peptideatlas.org/PASS/PASS01110）免费下载。
