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Configuration File
Yasset Perez-Riverol edited this page May 17, 2020
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It can be generated a template configuration file using the following command:
java -jar lucxor-{version}.jar -t
## Input file for Luciphor2 (aka: LucXor).
## Anything after a hash '#' is ignored
## By default, these initial parameters are for performing a phosphorylation search
SPECTRUM_PATH = <fill_in> ## specify the path to the spectra here
SPECTRUM_SUFFIX = MGF ## available options are MGF, mzML, or mzXML
## Specify your input PSM results format
INPUT_DATA = <fill_in> ## specify the path to the pepXML or tab-delimited file here
INPUT_TYPE = 0 ## 0 = TPP pepXML, 1 = tab-delimited file
ALGORITHM = 0 ## 0 = CID method, 1 = HCD method
TSV_HEADER = 0 ## This pertains ONLY to tab-delimited (TSV) input data
## 0 = the input file does NOT contain column names as the first row
## 1 = the first row of the input file is the column names
MS2_TOL = 0.5 ## MS/MS fragment ion tolerance
MS2_TOL_UNITS = 0 ## 0 = Daltons, 1 = PPM
MIN_MZ = 150.0 ## do not consider peaks below this value for matching fragment ions
OUTPUT_FILE = ## Specify the path to your desired output filename here
## A default value will be used if nothing is specified here.
WRITE_MATCHED_PEAKS_FILE = 0 ## Generate a tab-delimited file of all the matched peaks
## for the top 2 predictions of each spectra
## Useful for plotting spectra
## 0 = no, 1 = yes
## Place here any FIXED modifications that were used in your search
## This field is ONLY used for tab-delimited input
## Syntax: FIXED_MOD = <RESIDUE> <MODIFICATION_MASS>
## For N-terminal modifications use '[' for the residue character
## For C-terminal modifications use ']' for the residue character
FIXED_MOD = C 57.021464
## Place here any VARIABLE modifications that might be encountered that you don't
## want luciphor to score.
## This field is ONLY used for tab-delimited input
## Syntax: VAR_MOD = <RESIDUE> <MODIFICATION_MASS>
## For N-terminal modifications use '[' for the residue character
## For C-terminal modifications use ']' for the residue character
VAR_MOD = M 15.994915
## List the amino acids to be searched for and their mass modifications
## Syntax: TARGET_MOD = <RESIDUE> <MODIFICATION_MASS>
TARGET_MOD = S 79.966331
TARGET_MOD = T 79.966331
TARGET_MOD = Y 79.966331
## 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>
#NL = STE -H2O -18.01056 ## a correctly formatted example, (not actually recommended for phospho-searches)
#NL = RKQN -NH3 -17.026548 ## another correctly formatted example, (again not recommended for phospho-searches)
NL = sty -H3PO4 -97.97690
DECOY_MASS = 79.966331 ## 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 -<NEUTRAL_LOSS_MOLECULAR_FORMULA> <MASS_LOST>
DECOY_NL = X -H3PO4 -97.97690
MAX_CHARGE_STATE = 5 ## do not consider PSMs with a charge state above this value
MAX_PEP_LEN = 40 ## restrict scoring to peptides with a length shorter than this value
MAX_NUM_PERM = 16384 ## the maximum number of permutations a sequence can have
SELECTION_METHOD = 0 ## 0 = Peptide Prophet probability (default)
## 1 = Mascot Ion Score
## 2 = -log(E-value)
## 3 = X!Tandem Hyperscore
## 4 = Sequest Xcorr
MODELING_SCORE_THRESHOLD = 0.95 ## Minimum score a PSM needs to be considered for modeling
## The default assumes you are using SELECTION_METHOD=0
## If using SELECTION_METHOD=2 then set this value to your desired e-value it will be converted to -log(e-value) internally
SCORING_THRESHOLD = 0 ## PSMs below this value will be discarded
## Again, if using SELECTION_METHOD=2 then set this value to your desired e-value it will be converted to -log(e-value) internally
MIN_NUM_PSMS_MODEL = 50 ## The minimum number of PSMs you need for any charge state in order to build a model for it
MOD_PEP_REP = 0 ## 0 = show single character modifications, 1 = show TPP-formatted modifications
NUM_THREADS = 0 ## For multi-threading, zero = use all CPU found by JAVA
RUN_MODE = 0 ## Determines how Luciphor will run.
## 0 = Default: 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
## This option can be used to help diagnose problems with Luciphor. Multi-threading is disabled in debug mode.
DEBUG_MODE = 0 ## 0 = default: turn off debugging
## 1 = write peaks selected for modeling to disk
## 2 = write the scores of all permutations for each PSM to disk
## 3 = write the matched peaks for the top scoring permutation to disk
## 4 = write HCD non-parametric models to disk (HCD-mode only option)
This option can be used to help diagnose problems with Luxor. Multi-threading is disabled in debug mode.
DEBUG_MODE = 0 ## 0 = default: turn off debugging
## 1 = write peaks selected for modeling to disk
## 2 = write the scores of all permutations for each PSM to disk
## 3 = write the matched peaks for the top scoring permutation to disk
## 4 = write HCD non-parametric models to disk (HCD-mode only option)
- 0 = CID method
- 1 = HCD method
ALGORITHM = 0
The decoy mass is the PTM localization mass that is added to aminoacids to simulate a target-decoy approach:
DECOY_MASS = 79.966331 ## how much to add to an amino acid to make it a decoy
Some Peptide information is used to filter out PSMSs that are used to estimate the localization score. Those peptides will be skipped.
MAX_CHARGE_STATE = 5 ## do not consider PSMs with a charge state above this value
MAX_PEP_LEN = 40 ## restrict scoring to peptides with a length shorter than this value
The Scoring Threshold is used to select the PSMs that are used to model the LucXor score. In order to estimate accurately the LucXor score at least 50 PSM for a specific charge state should be available.
MAX_NUM_PERM = 16384 ## the maximum number of permutations a sequence can have
SCORING_THRESHOLD = 0 ## PSMs below this value will be discarded
## Again, if using SELECTION_METHOD=2 then set this value to your desired e-value it will be converted to -log(e-value) internally
MIN_NUM_PSMS_MODEL = 50 ## The minimum number of PSMs you need for any charge state in order to build a model for it