LAUSR.org creates dashboard-style pages of related content for over 1.5 million academic articles. Sign Up to like articles & get recommendations!

Data-Dependent Scoring Parameter Optimization in MS-GF+ Using Spectrum Quality Filter.

Photo by visuals from unsplash

Most database search tools for proteomics have their own scoring parameter sets depending on experimental conditions such as fragmentation methods, instruments, digestion enzymes, and so on. These scoring parameter sets… Click to show full abstract

Most database search tools for proteomics have their own scoring parameter sets depending on experimental conditions such as fragmentation methods, instruments, digestion enzymes, and so on. These scoring parameter sets are usually predefined by tool developers and cannot be modified by users. The number of different experimental conditions grows as the technology develops, and the given set of scoring parameters could be suboptimal for tandem mass spectrometry data acquired using new sample preparation or fragmentation methods. Here we introduce a new approach to optimize scoring parameters in a data-dependent manner using a spectrum quality filter. The new approach conducts a preliminary search for the spectra selected by the spectrum quality filter. Search results from the preliminary search are used to generate data-dependent scoring parameters; then, the full search over the entire input spectra is conducted using the learned scoring parameters. We show that the new approach yields more and better peptide-spectrum matches than the conventional search using built-in scoring parameters when compared at the same 1% false discovery rate.

Keywords: search; scoring parameter; scoring parameters; quality filter; spectrum quality; data dependent

Journal Title: Journal of proteome research
Year Published: 2018

Link to full text (if available)


Share on Social Media:                               Sign Up to like & get
recommendations!

Related content

More Information              News              Social Media              Video              Recommended



                Click one of the above tabs to view related content.