Additional file 2: of Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates

Table S1. The table is organized in the following spreadsheets: Spreadsheet “All Phosphopeptides”: This table lists all identified phosphopeptides from three independent replicates, via LC-MS/MS. Additional information corresponding to each phosphopeptide is also shown and includes peptide ID# (numerical ID), fraction (enriched; 1 or flowthrough; 2 fractions), Retention time, m/z, charge, measured mass, mass error, score, peptide sequence, modifications (type of PTM), UniProt accession, Phosphosite(s), sequence window, description of protein, use in quantitation (at least 2 unique tryptic peptides were identified for the corresponding protein), ANOVA p-values corresponding to each phosphopeptide identified across the three independent replicates, normalized abundance (phosphopeptide intensity) of the identified phosphopeptides across each replicate, average phosphopeptide intensities of the peptide in the control cells or cells expressing wild type SRMS, fold-change abundance of phosphopeptide intensities in SRMS-expressing cells (SRMS/Control) and Log2-scaled fold-change of SRMS/control values. Spreadsheet “All unique phosphoproteins”: This table lists all the unique phosphoproteins mapped from the phosphopeptides quantified via LC-MS/MS in the Vector and SRMS-expressing cells. Also shown are all associated phosphosites identified for each protein. Spreadsheet “Phosphopeptides p-value ≤ 0.05”: This table lists all phosphopeptides filtered at an ANOVA p-value threshold of 0.05. Also shown is other relevant information corresponding to each phosphopeptide, as in Spreadsheet “All Phosphopeptides”. Spreadsheet “Hyperphosphorylated proteins”: This table lists all the hyperphosphorylated/upregulated proteins identified in the SRMS-regulated phosphoproteome. These proteins were mapped from the hyperphosphorylated/upregulated peptides (Log2 SRMS/Control ≥1.58 and ANOVA p-value ≤0.05). Therefore, only phosphosites identified at Log2 SRMS/Control ≥1.58 and ANOVA p-value ≤0.05, are shown for every protein. Spreadsheet “Hypophosphorylated proteins”: Shown here is the hypophosphorylated/downregulated protein mapped from the hypophosphorylated/downregulated peptide (Log2 SRMS/Control ≤ − 1 and ANOVA p-value ≤0.05) identified in SRMS-expressing cells. (XLSX 745 kb)

表S1。本数据集包含以下工作表：
1. 工作表"所有磷酸化肽段（All Phosphopeptides）"：本列表收录了三次独立生物学重复实验经液相色谱-串联质谱（LC-MS/MS）鉴定得到的全部磷酸化肽段，同时附带每条磷酸化肽段的相关信息，包括：肽段ID（数字编号）、组分（富集组分为1，穿透组分为2）、保留时间、质荷比（m/z）、电荷数、实测质量、质量偏差、评分、肽段序列、修饰信息（翻译后修饰（Post-translational modification, PTM）类型）、UniProt登录号、磷酸化位点、序列窗口、蛋白质描述、定量适用性（对应蛋白质需至少鉴定到2条独特的胰蛋白酶肽段方可被用于定量分析）、三次独立生物学重复实验中每条磷酸化肽段的方差分析（ANOVA）p值、各重复实验中磷酸化肽段的归一化丰度（磷酸化肽段信号强度）、对照细胞或表达野生型SRMS的细胞中该肽段的平均信号强度、SRMS表达细胞与对照细胞的磷酸化肽段信号强度倍数变化（SRMS/对照），以及SRMS/对照值的以2为底的对数转换倍数变化。
2. 工作表"所有独特磷酸化蛋白质（All unique phosphoproteins）"：本列表收录了从空载体（Vector）转染细胞与SRMS过表达细胞中经LC-MS/MS定量的磷酸化肽段所映射得到的全部独特磷酸化蛋白质，同时附带每个蛋白质所鉴定到的全部相关磷酸化位点。
3. 工作表"p值≤0.05的磷酸化肽段（Phosphopeptides p-value ≤ 0.05）"：本列表收录了经方差分析（ANOVA）p值阈值0.05过滤后的全部磷酸化肽段，同时附带与"所有磷酸化肽段"工作表一致的相关信息。
4. 工作表"磷酸化水平上调蛋白质（Hyperphosphorylated proteins）"：本列表收录了SRMS调控的磷酸化蛋白质组中鉴定得到的全部磷酸化上调/丰度上调蛋白质，此类蛋白质由满足Log₂(SRMS/对照)≥1.58且ANOVA p值≤0.05的磷酸化上调/丰度上调肽段映射得到，因此每个蛋白质仅展示符合上述阈值条件的磷酸化位点。
5. 工作表"磷酸化水平下调蛋白质（Hypophosphorylated proteins）"：本列表收录了从SRMS过表达细胞中鉴定得到的磷酸化下调/丰度下调肽段（Log₂(SRMS/对照)≤-1且ANOVA p值≤0.05）所映射得到的全部磷酸化下调/丰度下调蛋白质。（XLSX 745 kb）