A Model to Determine Molecular Weights of Proteins from Gel Electrophoresis

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A Model to Determine Molecular Weights of
Proteins from Gel Electrophoresis

• By
• Jose Ceja
• Kamyar Ghods
• CSUN/JPL-PAIR 2001

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Outline

• Getting the data (Standards)
• Choosing a Model
• Getting the data (Unknowns)
• Applying the model
• Results and conclusions

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Getting the Data

• Two Methods were used
• Adobe Photoshop
• Spot Viewer

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Choosing a Model

• Cubic of form log(MW)ab(RM)2c(RM)3
• Cubic of form log(MW)ab(log(RM))2c(log(RM))3
  
• Quad Cross Validation of form log(MW)ab(RM)c(R
  M)2
• SLIC

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R-squared values
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Cross Validation
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Applying Our Model

• Collected unknown data using Photoshop
• Spot viewer not designed for 1D gels and not well
  understood.

• Applied best cubic model to
• each gel.

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Applying Our Model

• Created an average of our two data sets
• Applied cubic model to all
• Each standard had 3 cubic fits
• Used data that had the best cubic fit for each
  standard

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Joses Unknown

• Frog skin Gels _at_ 7 and 12 for males and females
• Within the same gel different lanes had different
  bands.
• Male and Female frogs skin do not have the exact
  same proteins

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Komys Unknown

• Comparing 3 methods
• Overall the Manual method found the most proteins
  and the Amylase method found the least.
• The replicates of each gel were pickkin up more
  and different proteins.

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Conclusions Future Work

• We both found that the higher concentrations
  found more proteins.
• Photoshop is more reliable for dense 1D gels.
• Out of the four models we tried, the cubic model
  was the best one.
• Further study is needed to find a true function
  relating RM to MW.

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Aknowledgements

• We thank CSUN/JPL-PAIR program, especially Dr.
  Carrol, Dr. Clevenson, Dr. Shubin, V. Hutchins
  and J. Handy.
• And our fellow students

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Residuals