The MSPepSearch node searches spectrum libraries downloaded from the National Institute of Standards and Technology (NIST) and other sources.
For information on using the MSPepSearch node in a workflow, see Working with spectrum library searches.
For information about administrative settings the MSPepSearch node, see MSPepSearch node configuration parameters.
The MSPepSearch node reports three scores:
- The MSPepSearch score, which is the MSPepSearch node’s main score
- The dot score, which is the score from a cross-correlation computed between two spectra
- The reverse dot score, which is the reversed spectral dot product
The following table describes the MSPepSearch node’s parameters, which are advanced parameters.
Parameters | Description |
|---|---|
Input Data |
|
Spectral Library | Specifies the name of the spectrum library to be searched. Displays only spectrum libraries compatible with MSPepSearch. |
Protein Database | Specifies the name of the protein sequence database used to link the identified peptides to proteins. |
The node supports up to 10 pairs of spectral libraries and protein databases. | |
Search Settings |
|
Precursor Mass Tolerance | Specifies the tolerance used for the precursor peptide. Range: 0.0001–5.0 Da or 0.01–5000 ppm; default: 10 ppm |
Fragment Mass Tolerance | Specifies the tolerance used in fragment matching. Range: 0.1–2.0 Da; default: 0.3 Da |
Min. Peak Intensity | Specifies a threshold intensity for peaks to be considered in the matching of the spectra. Does not consider peaks below this intensity. Range: 1–999; default: 1 |