PICquant-An integrated platform for biomarker discovery

PICquant-生物标志物发现的集成平台

• 批准号: 7669100
• 负责人: DENNIS J TEMPLETON
• 金额: $ 29.42万
• 依托单位: UNIVERSITY OF VIRGINIA
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-27 至 2010-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7669100
• 关键词: Algorithms; Appointment; Back; Biological Markers; Biopsy; Breast Carcinoma; Cancer Patient; Cataloging; Catalogs; Charge; Chemistry; Clinical; Clinical Research; Code; Complex; Complex Mixtures; Computer software; Computerized Medical Record; Coupled; Custom; Data; Data Analyses; Databases; Detection; Development; Diagnosis; Disease Clusterings; Ductal; Elements; Ensure; Equipment; Familiarity; Family; Funding; Future; Future Generations; Gene Expression; Health Insurance Portability and Accountability Act; Health Sciences; Home environment; Human; Individual; Ions; Irrigation; Label; Laboratories; Link; Malignant Neoplasms; Marker Discovery; Mass Spectrum Analysis; Measurement; Medical; Medical center; Outcome; Oxidation-Reduction; Pathologist; Pathology; Patients; Peptides; Principal Investigator; Procedures; Process; Protein Family; Proteins; Proteome; Proteomics; Protocols documentation; Public Health; Reagent; Records; Recruitment Activity; Registries; Research; Research Ethics Committees; Research Personnel; Resources; Running; Sampling; Scientist; Sequence Analysis; Series; Signal Pathway; Software Design; Specimen; Technology; Test Result; Testing; Training; Universities; Urine; Virginia; Work; base; cancer diagnosis; common rule; experience; follow-up; instrumentation; liquid chromatography mass spectrometry; mass spectrometer; medical information system; overexpression; prescription procedure; process optimization; programs; prospective; protein aminoacid sequence; protein expression; repository; research study; response; stable isotope; tool

DESCRIPTION (provided by applicant): Urine is an easily accessed specimen that has not been well exploited for cancer biomarker studies. We have developed a new stable isotope mass tag (13C Phenylisocyanate, PIC) that has several advantages for protein quantification in complex mixtures. We describe a complete analytic platform for urine biomarker discovery using PIC labeling. This platform includes: 1) custom designed software (PICquant) to automatically quantify labeled peaks, 2) a spectrum-comparison algorithm that groups spectra into a Registry of spectra representing unique peptide families, and 3) enhanced peptide sequencing by distinguishing b- and y-ion series in CID spectra. Completing the platform is a clinical registry that links acquired specimens to current and prospective clinical information including outcomes, and that enables multivariate clustering of disease states with quantified protein families. The mature PICquant platform will provide nearly completely automated data analysis, allowing assembly of numerous patient samples into complete protein abundance profiles akin to gene expression array data. Additionally, the expanding Registry database will be of use to other investigators processing either PIC-labeled or unlabeled peptide spectra.

描述（由申请人提供）： 尿液是一种容易获得的标本，尚未被很好地用于癌症生物标志物研究。我们已经开发了一种新的稳定同位素质量标签（13 C苯基异氰酸酯，PIC），具有几个优点，在复杂的混合物中的蛋白质定量。我们描述了一个完整的分析平台，尿液生物标志物发现使用PIC标记。该平台包括：1）定制设计的软件（PICquant），用于自动定量标记的峰，2）光谱比较算法，其将光谱分组为代表独特肽家族的光谱注册表，以及3）通过区分CID光谱中的B-和y-离子系列来增强肽测序。完成该平台是一个临床注册表，将采集的标本与当前和前瞻性临床信息（包括结果）联系起来，并使疾病状态与定量蛋白质家族的多变量聚类成为可能。成熟的PICquant平台将提供几乎完全自动化的数据分析，允许将大量患者样本组装成类似于基因表达阵列数据的完整蛋白质丰度谱。此外，扩大注册数据库将用于其他研究人员处理PIC标记或未标记的肽谱。

项目成果

MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

• DOI: 10.1016/j.jasms.2009.09.007
• 发表时间: 2010-01
• 期刊: Journal of the American Society for Mass Spectrometry
• 影响因子: 3.2
• 作者: Victor KG;Murgai M;Lyons CE;Templeton TA;Moshnikov SA;Templeton DJ
• 通讯作者: Templeton DJ

PICquant: a quantitative platform to measure differential peptide abundance using dual-isotopic labeling with 12C6- and 13C6-phenyl isocyanate.

PICquant：使用 12C6- 和 13C6- 异氰酸苯酯双同位素标记测量差异肽丰度的定量平台。

• DOI: 10.1021/ac102461e
• 发表时间: 2011
• 期刊: Analytical chemistry
• 影响因子: 7.4
• 作者: Lyons,CharlesE;Victor,KenG;Moshnikov,SergeyA;Bachmann,LorinM;Baras,AlexanderS;Dettmann,KathleenM;Cross,JanetV;Templeton,DennisJ
• 通讯作者: Templeton,DennisJ

Proteomic profile of reversible protein oxidation using PROP, purification of reversibly oxidized proteins.

使用 PROP 进行可逆蛋白质氧化的蛋白质组学分析，可逆氧化蛋白质的纯化。

• DOI: 10.1371/journal.pone.0032527
• 发表时间: 2012
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Victor,KenG;Rady,JoshuaM;Cross,JanetV;Templeton,DennisJ
• 通讯作者: Templeton,DennisJ