How does ProteinLynx Global Server calculate confidence limits for OK filters? - WKB9217

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• ProteinLynx Global Server

ANSWER

The principles are described in the following peer-reviewed papers, which are frequently cited by researchers publishing results generated using PLGS.

However, the score is not a hard value; it dependents on the data. A probability type of calculation, protein prophet like in terms of concept similarity, also attached, is conducted to provide a confidence level—green (>95% probability), amber (50-95% probability), red (< 50% probability).

Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures, Li et al. Proteomics 2009, 9, 1696–1719.

A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry. Nesvizhskii et al. Anal. Chem. 2003, 75, 4646-4658.

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