Search Engine Combination

Run a combination of peptide search engines. They will compare theoretical spectra from a protein database to experimental spectra in an mzML.

Options

XTandem: Run XTandem?
MSGFPlus: Run MSGFPlus?
Comet: Run Comet?
Allow unmatched peptides: Fail or warn if some found peptides do not match to the database?
Leucine/Isoleucine equivalent?: Consider amino acids Leucine and Isoleucine as equivalent since they cannot be distinguished by mass.
Precursor Mass Tolerance: Tolerance for matching masses of peptide sequences to fragment spectra for comparison.
Fragment mass Tolerance: Tolerance for matching observed peaks to theoretical peaks from insilico digest.
Min. peptide charge: Minimum charge of a peptide to be considered.
Max. peptide charge: Maximum charge of a peptide to be considered.
Min. peptide length: Minimum length (in aminoacids) of a peptide to be considered.
Max. peptide length: Maximum length (in aminoacids) of a peptide to be considered.
Max. nr. PSMs per spectrum: Maximum number of matches to report per fragment spectrum.
Max. nr. of variable modifications: Maximum number of variable modifications to consider per match.
Max. missed cleavages
Fixed modifications: Enter fixed modifications in OpenMS format: DBModname ([[Protein] N/C-term] Aminoacid)
Variable modifications: Enter variable modifications in OpenMS format: DBModname ([[Protein] N/C-term] Aminoacid)
Enzyme terminus specificity: Enter Description
ppm (or Da)?: Choose the unit for precursor tolerance.
ppm (or Da)?: Choose the unit for fragment tolerance.
Enzyme: Select enzyme.