The Spectrum Confidence Filter node sets up iterative searches. You can specify confidence levels for the purpose of re-searching all spectra that do not have a peptide identified with this confidence level. In the second search, you might apply wider tolerances, search against a bigger taxonomy, use other modifications, and so forth. The second search can therefore evaluate data that failed to meet the confidence level of the first search by using a different set of parameters—for example, evaluation with PTMs not included in the first search.

The following table describes the parameters for the Spectrum Confidence Filter node.

Spectrum Confidence Filter node parameters

Parameter

Definition

Spectrum Confidence

Specifies a confidence criterion and passes spectra with peptide matches that meet this criterion.

  • Equals: Passes spectra with peptide matches having the specified confidence level.
  • Better Than: Passes spectra with peptide matches having a confidence level better than the specified confidence level.
  • (Default) Worse Than: Passes spectra with peptide matches having a confidence level worse than the specified confidence level.
  • Low: Indicates a low-confidence peptide.
  • Medium: Indicates a medium-confidence peptide.
  • (Default) High: Indicates a high-confidence peptide.

Here are some examples:

  • If you set the Spectrum Confidence parameter to Worse Than High, the application passes all spectra with peptide spectrum matches having a confidence level worse than high.
  • If you set the Spectrum Confidence parameter to Better Than Low, the application passes all spectra with peptide spectrum matches having a confidence level better than low.
  • If you set the Spectrum Confidence parameter to Equal To Low, the application passes all spectra with peptide spectrum matches having a confidence level that is low.