Proteins identified from tumor-derived extracellular vesicles using mass spectrometry

Tumor-derived extracellular vesicles (tEVs) are important communication tools used by tumor cells to impact the function of other cells in the body. Accumulating evidence indicate that tEVs could impair the ability of immune cells in effectively attacking cancer cells. In our study, we find that proteins carried in tEVs are crucial for the immune-suppressive function of tEVs. In this study, we identified the proteins present in tEVs isolated from three different tumor cell lines: MCF7, A375, and A549. Proteins were extracted from the isolated tEVs, digested with trypsin, and analyzed by LC-MS/MS to identify the proteins. The identified proteins are listed in this dataset. Among the proteins identified, a total of 321 proteins were shared in all three tEVs, indicating tEVs use a core set of proteins to exert their suppressive function., Tumor-derived extracellular vesicles (tEVs) were isolated from A375, MCF7, and A549 tumor cells, respectively. Around 200 micrograms of proteins from each tEV sample were used for the proteomic analysis conducted at the Creative Proteomics Company. Proteins were precipitated using cold acetone, and the protein pellets were dissolved in 2 M urea. Samples were then treated with 10 mM DTT and incubated at 56 Celsius for 1 h followed by alkylation with 50 mM IAA. Concentrated ammonium bicarbonate was added into the solution to make a final concentration of 50 mM ammonium bicarbonate with pH of 7.8. Proteins in the samples were digested with trypsin at 37 Celsius for 15 h. The resulting peptides were purified with C18 SPE column to remove salt, resuspended in 20 microliters of 0.1% formic acid and subjected to LC-MS/MS analysis on Ultimate 3000 Nano UHPLC system. Data were analyzed and searched based on the human protein database using Maxquant (1.6.2.14)., , # Proteins identified from tumor-derived extracellular vesicles using mass spectrometry

[https://doi.org/10.5061/dryad.9s4mw6mrv](https://doi.org/10.5061/dryad.9s4mw6mrv)

## Description of the data and file structure

We have submitted our raw data (Proteins*Identified*fromtEVsviaMassSpectrometry.csv) that contain a list of proteins identified from the tEVs isolated from three different tumor cell lines. These cell lines are: MCF7 cell line, A375 cell line, and A549 cell line.

\"Protein names\" indicate the name of the protein identified from the corresponding tEVs;

\"Gene names\" indicate the corresponding gene name that encodes the protein.

The first two columns list the proteins and their gene names of tEVs from MCF7 cells;

The next two columns list the proteins and their gene names of tEVs from A375 cells;

The last two columns list the proteins and their gene names of tEVs from A549 cells.Â

# 基于质谱技术鉴定的肿瘤来源细胞外囊泡蛋白质
https://doi.org/10.5061/dryad.9s4mw6mrv

肿瘤来源细胞外囊泡（Tumor-derived extracellular vesicles, tEVs）是肿瘤细胞用于调控体内其他细胞功能的重要通讯载体。越来越多的研究证据表明，tEVs会削弱免疫细胞有效杀伤肿瘤细胞的能力。本研究发现，tEVs所载的蛋白质是其发挥免疫抑制功能的关键核心。本研究对源自三种不同肿瘤细胞系（MCF7、A375和A549）的tEVs所含蛋白质进行了鉴定：从分离得到的tEVs中提取蛋白质，经胰蛋白酶消化后通过液相色谱-串联质谱（LC-MS/MS）进行分析以完成蛋白质鉴定，本数据集收录了此次鉴定得到的所有蛋白质。在此次鉴定的蛋白质中，共有321种蛋白质在三种tEVs中均存在，提示tEVs通过一套核心蛋白质组来发挥其免疫抑制功能。

本研究分别从A375、MCF7和A549肿瘤细胞中分离得到tEVs。每份tEV样本取约200微克蛋白质，用于在Creative Proteomics公司开展的蛋白质组学分析。实验流程如下：采用冷丙酮沉淀蛋白质，将蛋白质沉淀重悬于2 M尿素溶液中；随后用10 mM二硫苏糖醇（DTT）处理样本，于56℃孵育1小时，再用50 mM碘乙酰胺（IAA）进行烷基化反应；向溶液中加入浓碳酸氢铵溶液，最终使体系中碳酸氢铵浓度达到50 mM、pH值为7.8；将样本中的蛋白质于37℃下用胰蛋白酶消化15小时；所得肽段经C18固相萃取（SPE）柱纯化以脱除盐类，重悬于20 μL 0.1%甲酸溶液中，随后在Ultimate 3000 Nano超高效液相色谱（UHPLC）系统上进行LC-MS/MS分析；使用Maxquant（1.6.2.14）软件，基于人类蛋白质数据库对数据进行分析与检索。

## 数据与文件结构说明
本研究已提交原始数据文件（Proteins*Identified*fromtEVsviaMassSpectrometry.csv），该文件包含从三种不同肿瘤细胞系（MCF7、A375和A549）分离得到的tEVs中鉴定出的蛋白质列表。

"Protein names"列对应从对应tEVs中鉴定得到的蛋白质名称；"Gene names"列对应编码该蛋白质的基因名称。

表格列分布如下：前两列分别为MCF7细胞来源tEVs的蛋白质名称及其基因名称；接下来两列为A375细胞来源tEVs的蛋白质名称及其基因名称；最后两列为A549细胞来源tEVs的蛋白质名称及其基因名称。