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.

Input Ports

Icon
Input spectra in mzML format
Icon
Input database in fasta format

Output Ports

Icon
IdXML files in a table
Icon
IdXML files in a File port

Nodes

Extensions

Links