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XTandemAdapter (version 2.8+galaxy0)

Input file containing MS2 spectra:

select mzml data sets(s)

FASTA file or pro file:

Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' select fasta data sets(s)

Default X:

Tandem configuration file. All parameters of this adapter take precedence over the file - use it for parameters not available here. A template file can be found at 'OpenMS/share/CHEMISTRY/XTandem_default_config.xml' select xml data sets(s)

Set this to use the configuration given in 'default_config_file' exclusively, ignoring other parameters (apart from 'in', 'out', 'database', 'xtandem_executable') set via this adapte:

Precursor mass tolerance:

Fragment mass erro:

Parent monoisotopic mass error units:

Fragment monoisotopic mass error units:

Maximum precursor charge ('0' to use X:

Tandem default)

By default, misassignment to the first and second isotopic 13C peak are also considered:

Set this flag to disable

Fixed modifications, specified using Unimod (www.unimod.org) terms:

e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'

Variable modifications, specified using Unimod (www.unimod.org) terms:

e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'

Minimum fragment m/z:

The enzyme used for peptide digestion:

Number of possible cleavage sites missed by the enzyme:

Require only peptide end to have a valid cleavage site, not both:

Which hits should be reported:

All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)

Maximal E-Value of a hit to be reported (only evaluated if 'output_result' is 'valid' or 'stochastic'):

Recalculate peptide to protein association using OpenMS:

Annotates target-decoy information

Advanced Options

Advanced Options 0

Optional outputs: