A Population-Size Model for Protein Spot Detection in Proteomic Studies

作者：Mao, Chang Xuan^*; Chen, Sining; Yang, Yitong

来源：Journal of Agricultural, Biological, and Environmental Statistics, 2016, 21(1): 170-180.

DOI：10.1007/s13253-015-0221-6

• Binomial mixture
• Capture-recapture
• Lower bounds
• Nonidentifiability

In proteomic studies, a population of proteins are often examined on a gel using a technique called two-dimensional gel eletrophoresis. The technique separates the protein population into individual protein spots on a two-dimensional gel by isoelectric charge and molecular weight. The resulting gel images are then processed by a software system for spot detection and subsequent analysis. The performance of a spot-detection program is evaluated by the total number of spots that are detected. A popular spot-detection program uses the "master-slave" approach, where all spots on "slave images" are subsets of the spots on the "master image." We argue that this approach potentially misses a large proportion of proteins and propose a model that quantifies the lack of performance. We provide nonparametric estimators for the protein population size and the expected number of proteins to be detected if a "fusion-gel" approach was used. Using the data from a rat liver proteome study, we estimate that more than half of the protein population is missed by the master-slave approach.

• 出版日期2016-3
• 单位上海财经大学