APEX Quantitative Proteomics Tool for Protein Quantification
Author Information
Author(s): Braisted John C, Kuntumalla Srilatha, Vogel Christine, Marcotte Edward M, Rodrigues Alan R, Wang Rong, Huang Shih-Ting, Ferlanti Erik S, Saeed Alexander I, Fleischmann Robert D, Peterson Scott N, Pieper Rembert
Primary Institution: J. Craig Venter Institute
Hypothesis
The APEX technique improves protein quantitation by correcting for variable peptide detection probabilities.
Conclusion
The APEX Quantitative Proteomics Tool allows for quick and accurate protein abundance estimation from LC-MS/MS datasets.
Supporting Evidence
- The APEX tool is a free open source Java application.
- It provides a graphical user interface for ease of use.
- The tool supports three primary processing tasks: training data construction, Oi value generation, and APEX abundance computation.
- It includes a Z-score analysis for identifying significant differential protein expression.
Takeaway
The APEX tool helps scientists measure how much protein is in a sample using special computer programs that analyze data from mass spectrometry.
Methodology
The APEX tool uses machine learning to predict peptide detection probabilities and computes protein abundance values from LC-MS/MS data.
Potential Biases
The training data may be biased towards non-observed peptides, affecting the classifier's performance.
Limitations
The accuracy of protein abundance estimates depends on the quality of peptide detection probabilities and the specific MS technology used.
Digital Object Identifier (DOI)
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