Galaxy |

LuciphorAdapter (version 2.8+galaxy0)

Input spectrum file:

select mzml data sets(s)

Protein/peptide identifications file:

select idxml data sets(s)

Fragmentation method:

Tolerance of the peaks in the fragment spectrum:

Unit of fragment mass tolerance:

Do not consider peaks below this value for matching fragment ions:

List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms:

e.g. 'Carbamidomethyl (C)'

List the types of neutral losses that you want to conside:

The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = - (space separated list, in order to allow for spaces in list items surround them by single quotes)

How much to add to an amino acid to make it a decoy:

For handling the neutral loss from a decoy sequence:

The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X - (space separated list, in order to allow for spaces in list items surround them by single quotes)

Do not consider PSMs with a charge state above this value:

Restrict scoring to peptides with a length shorter than this value:

Maximum number of permutations a sequence can have:

Minimum score a PSM needs to be considered for modeling:

PSMs below this value will be discarded:

The minimum number of PSMs you need for any charge state in order to build a model for it:

Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported:

Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used):

Advanced Options

Advanced Options 0

Optional outputs: