Brightness analysis

Patrick MacDonald, Jolene Johnson, Elizabeth Smith, Yan Chen, Joachim D. Mueller

Research output: Chapter in Book/Report/Conference proceedingChapter

23 Scopus citations


Brightness analysis provides a powerful tool for the study of protein interactions both in solution and in living cells. We provide a brief survey of some widely used techniques for extracting brightness from fluorescent fluctuation spectroscopy experiments. While all the techniques are equivalent under ideal conditions, we touch upon their relative strengths and discuss in detail a specific scenario wherein the photon-counting histogram (PCH) separates the brightness of rare, bright particles from a dominant background. In a practical vein for ensuring quantitative and unbiased brightness data, we address a number of potential issues stemming from both theoretical assumptions and experimental realities. Two additional issues arising from geometry are examined in greater detail. An oil-immersion objective skews the geometry of the excitation volume as a function of penetration depth. The bias can be characterized and corrected or avoided through the use of a water-immersion objective. Brightness measurements in thin sample geometries, frequently encountered in cells, may be biased. We use z-scan FFS to characterize sample geometry and correct any resulting bias in the brightness.

Original languageEnglish (US)
Title of host publicationFluorescence Fluctuation Spectroscopy (FFS), Part A
PublisherAcademic Press Inc.
Number of pages28
ISBN (Print)9780123884220
StatePublished - 2013

Publication series

NameMethods in Enzymology
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

Bibliographical note

Funding Information:
This work was supported by grants from the National Institutes of Health (GM64589 & GM091743) and the National Science Foundation (PHY-0346782).


  • Cumulant analysis
  • Fluorescence correlation spectroscopy
  • Photon-counting histogram
  • Protein-protein interactions
  • Stoichiometry


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