Data for: Urinary peptidome analyses for diagnosis of chronic kidney disease in dogs

CE-MS analyses were performed using a Beckman Coulter Proteome Lab PA800 capillary electrophoresis system (Beckman Coulter, Fullerton, USA) on-line coupled to a micrOTOF II MS (Bruker Daltonic, Bremen, Germany). The electro-ionization sprayer (Agilent Technologies, Palo Alto, CA, USA) was grounded, and the ion spray interface potential was set to –4.5 kV. Data acquisition and MS acquisition methods were automatically controlled by the CE via contact-close-relays. Spectra were accumulated every 3 s, over a range of m/z 350 to 3000. In the next step the MosaiquesVisu software package was applied to deconvolute mass spectral ion peaks, because ionization produced ions at different charged states from the original urinary peptides. This deconvolution step groups these differently charged ions into single peptides with unique real mass. Only signals observed in a minimum of three consecutive spectra with a signal-to-noise ratio of at least 4 were considered. Signals with a calculated charge of 1+ were automatically excluded to minimize interference with matrix compounds or drugs. Capillary electrophoresis migration time and MS-detected mass were normalized by the definition of 950 clusters of peptides covering a range of 17.23 to 47.74 minutes in CE migration time and 807 to 16399 kDa in molecular mass. Samples were normalized by peptide abundance (intensity) calibration based on 141 endogenous internal urinary polypeptide standards displaying the highest frequency and stability in all analysed samples, to compensate for differences in hydration status and urine volume between dogs. Each polypeptide present in the list was defined by its normalized migration time [min], molecular mass [kDa], and signal intensity detected. Using a Microsoft Structured Query Language database, all detected polypeptides were deposited, matched, and annotated in order to allow for further comparison between groups. The criteria applied to consider a polypeptide identical was that within different samples, the mass deviation was lower than 50 ppm for masses < 4 kDa, 150 ppm for masses >6 kDa, and between 50-150 ppm for masses between 4 and 6 kDa. Acceptable migration time deviation was between 1 and 2.5 minutes.

采用贝克曼库尔特蛋白质组实验室PA800毛细管电泳系统（贝克曼库尔特，富尔顿，美国）联用微流OTOF II质谱仪（布鲁克达尔顿尼克，不来梅，德国）进行CE-MS分析。电喷雾（安捷伦科技公司，帕洛阿尔托，加利福尼亚，美国）接地，并设置离子喷雾接口电势为-4.5 kV。数据采集和质谱采集方法由CE通过接触式继电器自动控制。光谱每3秒积累一次，范围在m/z 350至3000之间。在下一步中，应用MosaiquesVisu软件包对质谱离子峰进行解卷积，因为电离从原始尿液肽中产生了不同电荷状态的离子。此解卷积步骤将这些不同电荷的离子组合成具有独特真实质量的单个肽。只有观察到至少三个连续光谱且信噪比至少为4的信号才被考虑。计算出的电荷为1+的信号自动排除，以最大限度地减少与基质化合物或药物的干扰。通过定义覆盖17.23至47.74分钟CE迁移时间和807至16399 kDa分子质量范围的950个肽簇，对毛细管电泳迁移时间和MS检测到的质量进行归一化。通过基于141个在所有分析样本中频率和稳定性最高的内源性尿液多肽标准的肽丰度（强度）校准，对样本进行归一化，以补偿狗之间水分状态和尿液体积的差异。列表中的每种多肽均由其归一化迁移时间[分钟]、分子质量[kDa]和检测到的信号强度定义。使用微软结构化查询语言数据库，将所有检测到的多肽存档、匹配和注释，以便进行组间进一步比较。考虑多肽相同的标准是，在不同样本中，质量偏差小于50 ppm（质量小于4 kDa）、150 ppm（质量大于6 kDa）和介于50-150 ppm（质量介于4和6 kDa之间）。可接受的迁移时间偏差在1至2.5分钟之间。