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Published on: October 28, 2021
Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors
Boris L Zybailov1, Laurence Florens, Michael P Washburn
1Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA.
Molecular Biosystems
|April 27, 2007
Summary
This study demonstrates proteinase K
Area of Science:
- Proteomics
- Biochemistry
Background:
- Non-specific proteases are typically avoided in quantitative proteomics due to high false discovery rates.
- However, they can improve sequence coverage for difficult-to-access proteins.
Purpose of the Study:
- To evaluate the utility of proteinase K, a non-specific protease, for quantitative proteomics.
- To assess protein expression differences in Saccharomyces cerevisiae using this method.
Main Methods:
- Quantitative shotgun proteomics using proteinase K.
- Analysis of Saccharomyces cerevisiae grown in 14N and 15N media.
- Quantification using normalized spectral abundance factors (NSAFs) and statistical analysis via t-test after log transformation.
Main Results:
- A dataset of 719 unique proteins was identified across three biological replicates.
- 84 proteins exhibited statistically significant expression differences between growth conditions.
- Log-transformed NSAF values followed a normal distribution, enabling robust statistical analysis.
Conclusions:
- Proteinase K can be effectively used for quantitative proteomics, offering improved sequence coverage.
- This approach allows for reliable identification and quantification of differential protein expression.
