LuciphorAdapter

Options

version

Version of the tool that generated this parameters file.

fragment_method

Fragmentation method

fragment_mass_tolerance

Tolerance of the peaks in the fragment spectrum

fragment_error_units

Unit of fragment mass tolerance

min_mz

Do not consider peaks below this value for matching fragment ions

target_modifications

List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)'

neutral_losses

List the types of neutral losses that you want to consider. 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 = <RESDIUES> -<NEUTRAL_LOSS_MOLECULAR_FORMULA> <MASS_LOST>

decoy_mass

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

decoy_neutral_losses

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 -<NEUTRAL_LOSS_MOLECULAR_FORMULA> <MASS_LOST>

max_charge_state

Do not consider PSMs with a charge state above this value

max_peptide_length

Restrict scoring to peptides with a length shorter than this value

max_num_perm

Maximum number of permutations a sequence can have

modeling_score_threshold

Minimum score a PSM needs to be considered for modeling

scoring_threshold

PSMs below this value will be discarded

min_num_psms_model

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

num_threads

For multi-threading, 0 = use all CPU found by JAVA

run_mode

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

rt_tolerance

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

java_memory

Maximum Java heap size (in MB)

java_permgen

Maximum Java permanent generation space (in MB); only for Java 7 and below

log

Name of log file (created only when specified)

debug

Sets the debug level

threads

Sets the number of threads allowed to be used by the TOPP tool

no_progress

Disables progress logging to command line

force

Overrides tool-specific checks

test

Enables the test mode (needed for internal use only)

Views

LuciphorAdapter Std Output

The text sent to standard out during the execution of LuciphorAdapter.

LuciphorAdapter Error Output

The text sent to standard error during the execution of LuciphorAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

• Phosphoproteomics_IDKNIME Hub
• Phosphoproteomics_IDOpenMS

Links

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Developers