Galaxy |

MSGFPlusAdapter (version 2.8+galaxy0)

Input file (MS-GF+ parameter '-s'):

select mgf,ms2,mzml,mzxml data sets(s)

Protein sequence database (FASTA file; MS-GF+ parameter '-d'):

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

Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t'):

Unit of precursor mass tolerance (MS-GF+ parameter '-t'):

Range of allowed isotope peak errors (MS-GF+ parameter '-ti'):

Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| < 20 ppm' for n = -1, 0, 1, 2

Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m'):

Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst'):

Enzyme used for digestion, or type of cleavage:

Note: MS-GF+ does not support blocking rules. (MS-GF+ parameter '-e')

Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p'):

Level of cleavage specificity required (MS-GF+ parameter '-ntt'):

Minimum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-minCharge'):

Maximum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-maxCharge'):

Minimum peptide length to consider (MS-GF+ parameter '-minLength'):

Maximum peptide length to consider (MS-GF+ parameter '-maxLength'):

Number of matches per spectrum to be reported (MS-GF+ parameter '-n'):

Output additional features (MS-GF+ parameter '-addFeatures'):

This is required by Percolator and hence by default enabled

Maximum number of modifications per peptide:

If this value is large, the search may take very long

Maximum number of missed cleavages allowed for a peptide to be considered for scoring:

(default: -1 meaning unlimited)

(Override the number of tasks to use on the threads; Default: (internally calculated based on inputs)):

More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs).. 1 <= tasks <= numThreads: will create one task per thread, which is the original behavior.. tasks = 0: use default calculation - minimum of: (threads*3) and (numSpectra/250).. tasks < 0: multiply number of threads by abs(tasks) to determine number of tasks (i.e., -2 means "2 * numThreads" tasks).. One task per thread will use the most memory, but will usually finish the fastest.. 2-3 tasks per thread will use comparably less memory, but may cause the search to take 1.5 to 2 times as long

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)'

Optional MSGF+ configuration file (passed as -conf to MSGF+):

See documentation for examples. Parameters of the adapter take precedence. Use conf file only for settings not available here (for example, any fixed/var modifications, in the conf file will be ignored, since they are provided via -mod flag) select txt data sets(s)

Recalculate peptide to protein association using OpenMS:

Annotates target-decoy information

Advanced Options

Advanced Options 0

Optional outputs: