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Combining percolator with X!Tandem for accurate and sensitive peptide identification.
Mingguo Xu1, Zhendong Li, Liang Li
1Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
Journal of Proteome Research
|April 16, 2013
Summary
We developed X!Tandem Percolator, an enhanced platform for peptide identification. This tool improves proteomic data analysis by increasing the number of accurate peptide identifications, boosting sensitivity and specificity.
Area of Science:
- Proteomics
- Bioinformatics
- Computational Biology
Background:
- X!Tandem is a widely used software for peptide identification in mass spectrometry.
- Percolator is a tool for re-scoring peptide identifications to improve accuracy.
- Interfacing these tools can enhance proteomic data analysis.
Purpose of the Study:
- To develop an improved search platform by interfacing Percolator with X!Tandem.
- To enhance the classification performance of peptide identifications.
- To increase the sensitivity and specificity of proteomic data analysis.
Main Methods:
- Developed X!Tandem Percolator by interfacing Percolator with X!Tandem using a PHP program.
- Utilized 34,993 experimentally validated spectral identifications to guide feature selection.
- Compared features of validated and false peptide matches (e.g., Log(E), mass error) for objective criteria.
- Assessed accuracy by comparing estimated q-values with empirical q-values.
Main Results:
- Demonstrated superior sensitivity and specificity of X!Tandem Percolator compared to original X!Tandem.
- Showed improved number of peptide identifications at the same q-value levels across various datasets.
- Validated the accuracy of X!Tandem Percolator using a validated dataset.
Conclusions:
- X!Tandem Percolator offers a significant improvement over standard X!Tandem for peptide identification.
- The developed platform enhances the reliability and depth of proteomic analyses.
- Objective feature selection based on validated data improves classification performance.
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