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The first step in analyzing an mass spectrometry assay is to match the harvested spectra against a target database using database search engines such as Sequest and Mascot, a process that renders list of peptide-spectrum matches. However, it is not trivial to assess the accuracy of these identifications.
Percolator uses a semi-supervised machine learning to discriminate correct from incorrect peptide-spectrum matches, and calculates accurate statistics such as q-value (FDR) and posterior error probabilities.
How to:
download and install percolator
run a test example
cite percolator
Here you can read about Percolator’s:
license
input formats
Getting started
Home
Download and Install
Example
User guide
Command line options
Interface
Advanced topics
Decoys
Post translational Modifications (PTMs)
Protein inference
PSM deduplication
Additional info
Licenses
How to cite Percolator
Software that use percolator