Relative signal intensities of NUP peptides in pre-labeling KARMA assay samples

Supplementary analyzed data from Manuscript: TITLE: Maturation kinetics of a multiprotein complex revealed by metabolic labeling. JOURNAL: CELL. Article Type: Research Article Authors: Evgeny Onischenko*, Elad Noor*, Jonas S. Fischer*, Ludovic Gillet, Matthias Wojtynek, Pascal Vallotton, Karsten Weis *Equally Contributing Authors Corresponding Authors: Evgeny Onischenko and Karsten Weis Related to Figure S2; Table S4 Relative signal intensities of NUP peptides in pre-labeling KARMA assay samples. The target protein complex is isolated from cell lysates by affinity pulldowns, tryptically digested and analyzed with LC-MS on an Orbitrap mass-spectrometer. The MS2 fragmentation spectra are acquired in a DIA mode for all samples. Peptide intensities are extracted from the DIA datasets with Spectronaut software (Biognosis) using complementary assay spectral libraries. Individual plots: The fraction of protein's signal intensity in each sample (red track) is given by the median of the signal fraction across all high quality precursor ions (green tracks). Low quality precursor ions (grey tracks) are excluded from quantification. x-axis: individual samples, y-axis: fraction of precursor ion signal in a sample (precursor signal intensity in a sample normalised for the total across all 34 samples). Individual precursor ion values across samples are connected, forming a track.

本补充分析数据来自下述学术论文：标题：《代谢标记揭示多蛋白复合物的成熟动力学》，期刊：《CELL》，文章类型：研究论文，作者：Evgeny Onischenko*、Elad Noor*、Jonas S. Fischer*、Ludovic Gillet、Matthias Wojtynek、Pascal Vallotton、Karsten Weis *同等贡献作者，通讯作者：Evgeny Onischenko与Karsten Weis。本数据关联补充图S2与补充表S4，内容为预标记KARMA测定（KARMA assay）实验样品中核孔蛋白（NUP，nucleoporin）肽段的相对信号强度。目标蛋白复合物通过亲和下拉（affinity pulldown）从细胞裂解液中分离，经胰蛋白酶酶解后，采用液相色谱-质谱联用（Liquid Chromatography-Mass Spectrometry, LC-MS）结合轨道阱质谱仪（Orbitrap mass-spectrometer）进行分析。所有样品均采用数据非依赖性采集（Data-Independent Acquisition, DIA）模式采集MS2碎裂谱图。肽段信号强度通过Spectronaut软件（Biognosis公司）结合配套的测定光谱库，从DIA数据集中提取得到。单幅绘图说明：每个样品中蛋白信号强度占比（红色轨迹）由该样品内所有高质量前体离子（绿色轨迹）的信号占比中位数计算得出；低质量前体离子（灰色轨迹）被排除于定量分析之外。横轴为单个样品，纵轴为单个样品中的前体离子信号占比（即该样品的前体信号强度经全部34个样品总信号归一化后的结果）。跨样品的单个前体离子数值被依次连接，形成轨迹线条。