A selected reaction monitoring mass spectrometric assessment of biomarker candidates diagnosing large-cell neuroendocrine lung carcinoma by the scaling method using endogenous references.
A selected reaction monitoring mass spectrometric assessment of biomarker candidates diagnosing large-cell neuroendocrine lung carcinoma by the scaling method using endogenous references.
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DOI：
10.1371/journal.pone.0176219
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Nishimura T
中科院分区：
文献类型：
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作者：
Fukuda T;Nomura M;Kato Y;Tojo H;Fujii K;Nagao T;Bando Y;Fehniger TE;Marko-Varga G;Nakamura H;Kato H;Nishimura T
进行基于选择反应监测质谱（SRM-MS）的半定量，以评估46种选择的候选蛋白质用于特异性诊断大细胞神经内分泌肺癌（LCNEC）并将其与其他肺癌亚型区分开来的有效性。在本研究中应用缩放方法，使用源自内源性参比蛋白的特定SRM峰面积（AUC），将候选蛋白获得的所有SRM AUC归一化。在筛选验证研究中，我们发现46个候选蛋白中的7个对于LCNEC表型具有统计学显著性，包括4F 2 hc细胞表面抗原重链（4F2hc/CD98）（p-ANOVA ≤ 0.0012），视网膜脱氢酶1（p-ANOVA ≤ 0.0029），载脂蛋白A-I（p-ANOVA ≤ 0.0004），β-烯醇化酶（p-ANOVA ≤ 0.0043），肌酸激酶B型（p-ANOVA ≤ 0.0070）、半乳糖凝集素-3结合蛋白（p-ANOVA = 0.0080）和磷脂酰乙醇胺结合蛋白1（p-ANOVA ≤ 0.0012）。此外，我们还鉴定了小细胞肺癌（SCLC）亚型特异性的候选蛋白。这些候选物包括脑酸可溶性蛋白1（p-ANOVA < 0.0001）和γ-烯醇化酶（p-ANOVA ≤ 0.0013）。这种新的基于相对定量的方法利用缩放方法，可以应用于评估从发现蛋白质组学研究中获得的数百种蛋白质候选物，作为生物标志物开发过程中验证阶段的第一步。
Selected reaction monitoring mass spectrometry (SRM-MS) -based semi-quantitation was performed to assess the validity of 46 selected candidate proteins for specifically diagnosing large-cell neuroendocrine lung carcinoma (LCNEC) and differentiating it from other lung cancer subtypes. The scaling method was applied in this study using specific SRM peak areas (AUCs) derived from the endogenous reference protein that normalizes all SRM AUCs obtained for the candidate proteins. In a screening verification study, we found that seven out of the 46 candidate proteins were statistically significant for the LCNEC phenotype, including 4F2hc cell surface antigen heavy chain (4F2hc/CD98) (p-ANOVA ≤ 0.0012), retinal dehydrogenase 1 (p-ANOVA ≤ 0.0029), apolipoprotein A-I (p-ANOVA ≤ 0.0004), β-enolase (p-ANOVA ≤ 0.0043), creatine kinase B-type (p-ANOVA ≤ 0.0070), and galectin-3-binding protein (p-ANOVA = 0.0080), and phosphatidylethanolamine-binding protein 1 (p-ANOVA ≤ 0.0012). In addition, we also identified candidate proteins specific to the small-cell lung carcinoma (SCLC) subtype. These candidates include brain acid soluble protein 1 (p-ANOVA < 0.0001) and γ-enolase (p-ANOVA ≤ 0.0013). This new relative quantitation-based approach utilizing the scaling method can be applied to assess hundreds of protein candidates obtained from discovery proteomic studies as a first step of the verification phase in biomarker development processes.
DOI：
10.1186/2043-9113-1-23
发表时间：
2011-09-03
期刊：
Journal of clinical bioinformatics
影响因子：
--
作者：
Nomura M;Fukuda T;Fujii K;Kawamura T;Tojo H;Kihara M;Bando Y;Gazdar AF;Tsuboi M;Oshiro H;Nagao T;Ohira T;Ikeda N;Gotoh N;Kato H;Marko-Varga G;Nishimura T
通讯作者：
Nishimura T