Bennett Keiryn L, Wang Xia, Bystrom Cory E, Chambers Matthew C, Andacht Tracy M, Dangott Larry J, Elortza Félix, Leszyk John, Molina Henrik, Moritz Robert L, Phinney Brett S, Thompson J Will, Bunger Maureen K, Tabb David L
From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria;
§University of Cincinnati, Department of Mathematical Sciences, University of Cincinnati, Cincinnati, Ohio, 45221-0025;
Mol Cell Proteomics. 2015 Dec;14(12):3299-309. doi: 10.1074/mcp.O115.051888. Epub 2015 Oct 4.
Questions concerning longitudinal data quality and reproducibility of proteomic laboratories spurred the Protein Research Group of the Association of Biomolecular Resource Facilities (ABRF-PRG) to design a study to systematically assess the reproducibility of proteomic laboratories over an extended period of time. Developed as an open study, initially 64 participants were recruited from the broader mass spectrometry community to analyze provided aliquots of a six bovine protein tryptic digest mixture every month for a period of nine months. Data were uploaded to a central repository, and the operators answered an accompanying survey. Ultimately, 45 laboratories submitted a minimum of eight LC-MSMS raw data files collected in data-dependent acquisition (DDA) mode. No standard operating procedures were enforced; rather the participants were encouraged to analyze the samples according to usual practices in the laboratory. Unlike previous studies, this investigation was not designed to compare laboratories or instrument configuration, but rather to assess the temporal intralaboratory reproducibility. The outcome of the study was reassuring with 80% of the participating laboratories performing analyses at a medium to high level of reproducibility and quality over the 9-month period. For the groups that had one or more outlying experiments, the major contributing factor that correlated to the survey data was the performance of preventative maintenance prior to the LC-MSMS analyses. Thus, the Protein Research Group of the Association of Biomolecular Resource Facilities recommends that laboratories closely scrutinize the quality control data following such events. Additionally, improved quality control recording is imperative. This longitudinal study provides evidence that mass spectrometry-based proteomics is reproducible. When quality control measures are strictly adhered to, such reproducibility is comparable among many disparate groups. Data from the study are available via ProteomeXchange under the accession code PXD002114.
关于蛋白质组学实验室纵向数据质量和可重复性的问题，促使生物分子资源设施协会蛋白质研究小组（ABRF-PRG）设计了一项研究，以系统评估蛋白质组学实验室在较长时间内的可重复性。作为一项开放研究开展，最初从更广泛的质谱学界招募了64名参与者，让他们在九个月的时间里每月分析提供的六份牛蛋白胰蛋白酶消化混合物的等分试样。数据上传至中央储存库，操作人员回答了一份随附的调查问卷。最终，45个实验室提交了至少8个以数据依赖型采集（DDA）模式收集的LC-MSMS原始数据文件。未强制执行标准操作规程；相反，鼓励参与者按照实验室的常规做法分析样品。与以往研究不同，这项调查并非旨在比较实验室或仪器配置，而是评估实验室内部的时间可重复性。研究结果令人安心，80%的参与实验室在9个月期间的分析具有中等至高可重复性和质量。对于有一个或多个异常实验的组，与调查数据相关的主要促成因素是LC-MSMS分析前的预防性维护情况。因此，生物分子资源设施协会蛋白质研究小组建议实验室在此类事件后仔细审查质量控制数据。此外，必须改进质量控制记录。这项纵向研究提供了基于质谱的蛋白质组学具有可重复性的证据。当严格遵守质量控制措施时，这种可重复性在许多不同组之间是可比的。该研究的数据可通过ProteomeXchange获取，登录代码为PXD002114。
