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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
Published on: November 15, 2017
msmsEval: tandem mass spectral quality assignment for high-throughput proteomics.
Jason W H Wong1, Matthew J Sullivan, Hugh M Cartwright
1Chemistry Department, Oxford University, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, UK. jason.wong@ucd.ie <jason.wong@ucd.ie>
BMC Bioinformatics
|February 13, 2007
Summary
A new tool, msmsEval, provides probability values to assess spectral quality in proteomics, improving protein identification efficiency. This method helps filter spectra, enabling more targeted and successful database searches for modified proteins.
Area of Science:
- Proteomics
- Computational Biology
- Mass Spectrometry Analysis
Background:
- Database search programs are standard for protein identification from tandem mass spectra.
- Growing sequence databases increase computational demands, especially for modified proteins.
- Existing spectral quality rankings use arbitrary cut-offs, limiting interpretability.
Purpose of the Study:
- To develop a statistically interpretable spectral quality statistic.
- To provide probability values for spectrum identifiability.
- To improve the efficiency of proteomics database searches.
Main Methods:
- Developed msmsEval application using a Gaussian mixture model to statistically model spectral quality.
- Implemented a probability-based filtering approach for spectra.
- Validated the method on a public dataset.
Main Results:
- msmsEval predicts spectral quality with associated probabilities.
- Identified spectra predicted as high-quality but unidentified are candidates for intensive searches.
- 83.9% of high-quality spectra predicted by msmsEval but missed by standard searches were interpretable.
Conclusions:
- msmsEval offers a statistically robust method for spectral quality assessment.
- The tool aids in filtering spectra for high-throughput proteomics projects.
- msmsEval is freely available for download and supports multiple operating systems.
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