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

Author

Listed:
  • Chang Xuan Mao

    (Shanghai University of Finance and Economics)

  • Sining Chen

    (Bell Labs)

  • Yitong Yang

    (Shanghai University of Finance and Economics)

Abstract

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.

Suggested Citation

  • Chang Xuan Mao & Sining Chen & Yitong Yang, 2016. "A Population-Size Model for Protein Spot Detection in Proteomic Studies," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 21(1), pages 170-180, March.
    • Handle: RePEc:spr:jagbes:v:21:y:2016:i:1:d:10.1007_s13253-015-0221-6
    DOI: 10.1007/s13253-015-0221-6
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    References listed on IDEAS

    as
    1. Xuan Mao, Chang, 2007. "Estimating population sizes for capture-recapture sampling with binomial mixtures," Computational Statistics & Data Analysis, Elsevier, vol. 51(11), pages 5211-5219, July.
    2. Gascuel, O. & Caraux, G., 1992. "Bounds on expectations of order statistics via extremal dependences," Statistics & Probability Letters, Elsevier, vol. 15(2), pages 143-148, September.
    3. Chang Xuan Mao & Robert K. Colwell & Jing Chang, 2005. "Estimating the Species Accumulation Curve Using Mixtures," Biometrics, The International Biometric Society, vol. 61(2), pages 433-441, June.
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