Additional file 2 of Mass spectrometric profiling of DNA adducts in the human stomach associated with damage from environmental factors

Additional file 2 Supplementary Table S1: Mass transitions of DNA adducts. Seven mass transitions that assume a neutral loss of 116 units of deoxyribose in DNA adducts of deoxyribonucleosides were monitored by mass spectrometry. Supplementary Table S2: Estimated molar ratios of DNA adducts in samples. As described in the Materials and Methods, the molar ratios of DNA adducts and three pairs of peak boundaries, namely, broad, best retention time (Best) and background (BG), were listed for each DNA adduct. A total of 341 samples were classified as GC (Case No. 1–59) and non-GC (Case No. 60–66). Samples from GC were also categorized as tumor or nontumor and are indicated in the Group Status column. Supplementary Table S3: Numbers of sampling sites. The number of samples per individual and its frequency are listed in the table of the nontumor portions of 59 GC cases. This is used to draw the histogram in Fig. 1b. Supplementary Table S4: Representative molar ratio of DNA adducts in individuals. Representative values of the molar ratio of DNA adducts in 59 cases of nontumor GC, 14 cases of tumor GC and 7 cases of non-GC were calculated. In addition to basic characteristics (age, sex, BMI, smoking, and alcohol), groups for comparison are indicated in Fig. 4 (Group Status) and Fig. 5 (Smoking Group, Alcohol Group and Smoking/Alcohol Group). To reduce redundancy, individual information for tumor samples was omitted, and the corresponding case number was indicated. Supplementary Table S5: Interindividual variance of DNA adducts. For the molar ratio of DNA adducts in 306 samples of nontumor gastric mucosae in 59 gastric cancer cases, the Kruskal-Wallis test was performed to compare individuals. Asymptotic significance calculated by SPSS software is displayed. The p-values less than 0.05 are marked in yellow. Supplementary Table S6: Normality test of the distribution of DNA adducts among individuals. The Shapiro-Wilk test was performed to determine the distribution of the representative molar ratio of DNA adducts in individuals. Cases with 0 values were excluded. The p-values less than 0.05 are marked in yellow. df: degrees of freedom. Supplementary Table S7: Accumulation of DNA adducts in tumor or nontumor sites of gastric mucosae. The Kruskal-Wallis test was performed to compare non-GC, GC nontumor and GC tumor samples. In the two DNA adducts showing p-values less than 0.05, Bonferroni-corrected pairwise Mann-Whitney U tests were also performed. The related box plots are drawn in Fig. 4. The p-values less than 0.05 are marked in yellow. Supplementary Table S8: Comparison of DNA adducts between sexes and among environmental exposure groups. The Mann-Whitney U test was performed to compare the molar ratio of DNA adducts in individuals with different characteristics, including sex, tobacco smoking, alcohol consumption and both habits. The data with p-values less than 0.05 are marked in yellow and are drawn as box plots in Fig. 5. Supplementary Table S9: Correlation analysis of age, BMI and 7 DNA adduct accumulations. Spearman’s rank correlation coefficient, rho and p-value were calculated pairwise among age, BMI and molar ratio of 7 DNA adducts. The p-values less than 0.05 are marked in yellow.

附加文件2 补充表S1：DNA加合物（DNA adducts）的质量跃迁。本研究通过质谱法（mass spectrometry）监测了7种针对脱氧核苷（deoxyribonucleosides）类DNA加合物、发生116单位脱氧核糖（deoxyribose）中性丢失的质量跃迁。

补充表S2：样品中DNA加合物的估算摩尔比（molar ratios）。如材料与方法部分所述，针对每种DNA加合物，均列出了其摩尔比，以及3组峰边界：宽峰、最佳保留时间（Best）峰与背景（BG）峰。本研究共纳入341例样本，分为胃癌（Gastric Cancer, GC）组（病例编号1–59）与非胃癌（non-GC）组（病例编号60–66）。胃癌组样本进一步按肿瘤组织与非肿瘤组织分类，该分类信息见于分组状态（Group Status）列。

补充表S3：采样位点数量。本表格列出了59例胃癌患者非肿瘤胃黏膜组织的样本数及其出现频率，用于绘制图1b的直方图（histogram）。

补充表S4：个体中DNA加合物的代表性摩尔比。本研究计算了59例胃癌非肿瘤组织、14例胃癌肿瘤组织与7例非胃癌样本的DNA加合物摩尔比代表值。除年龄、性别、体质量指数（Body Mass Index, BMI）、吸烟与饮酒史等基础特征外，用于分组比较的信息分别见于图4（分组状态）与图5（吸烟组、饮酒组及烟酒联合暴露组）。为减少冗余，肿瘤样本的个体信息已省略，仅标注对应病例编号。

补充表S5：个体间DNA加合物的变异度。针对59例胃癌患者的306份非肿瘤胃黏膜样本的DNA加合物摩尔比，本研究采用克鲁斯卡尔-沃利斯检验（Kruskal-Wallis test）进行个体间比较。由SPSS软件计算得到的渐近显著性值已列出，p值小于0.05的结果以黄色标注。

补充表S6：个体间DNA加合物分布的正态性检验。本研究采用夏皮罗-威尔克检验（Shapiro-Wilk test）分析个体DNA加合物代表性摩尔比的分布特征，剔除了数值为0的病例。p值小于0.05的结果以黄色标注。df：自由度（degrees of freedom）。

补充表S7：胃黏膜肿瘤与非肿瘤位点的DNA加合物蓄积情况。本研究采用克鲁斯卡尔-沃利斯检验比较非胃癌、胃癌非肿瘤与胃癌肿瘤三组样本的DNA加合物水平。针对其中p值小于0.05的2种DNA加合物，本研究进一步开展了邦费罗尼校正（Bonferroni-corrected）后的配对曼-惠特尼U检验（Mann-Whitney U test）。相关箱线图（box plots）已绘制于图4中，p值小于0.05的结果以黄色标注。

补充表S8：不同性别与环境暴露组间DNA加合物的比较。本研究采用曼-惠特尼U检验，针对不同性别、吸烟、饮酒及兼具烟酒暴露特征的个体，比较其DNA加合物摩尔比的差异。p值小于0.05的结果以黄色标注，并绘制为图5中的箱线图。

补充表S9：年龄、BMI与7种DNA加合物蓄积量的相关性分析。本研究针对年龄、BMI及7种DNA加合物摩尔比开展两两配对分析，计算得到斯皮尔曼等级相关系数（Spearman’s rank correlation coefficient）ρ与p值。p值小于0.05的结果以黄色标注。