Commandline options for Luciphor

This site list the commandline options that Luciphor recognizes.
Commands in red are advanced options and not recommended for general use.

Option Example Usage Description
-i -i interact.pep.xml Path to the input TPP pepXML file
-d -d /usr/local/tpp/data Path to the input spectra files. These files must match the names for the PSMs in the TPP pepXML file. Example PSM identifier from a pepXML file: ppeptidemix2_CID_Orbi.2022.2022.2
-w -w 0.5 The MS2 fragment ion tolerance in Daltons (default is 0.5 Da.)
-x -x 0 Peptide selection method. This option is used with -p and -m By default, Luciphor parses PSMs based upon their PeptideProphet probabilities. Other selection methods include:
  • 1 = SEQUEST/Commet Xcorr values
  • 2 = -log(X!Tandem E-value)
  • 3 = Mascot Ion Score
-p -p 0.05 Minimum peptide probability threshold for scoring PSMs. Any PSM with a probability at or above this value will be scored by Luciphor.
-m -m 0.95 Minimum peptide probability to use for parameter estimation. All PSMs with a probability at or above this value will be used for calculating the Luciphor modeling parameters.
-e -e mzXML The file extension for the input spectra files to be used by Luciphor. The default value is mzXML. Any of the mz* file formats supported by Proteowizard should be acceptable. MGF, DTA, and other text based files do not seem to be read correctly. (This will be fixed in future releases.)
-f -f "Full Monty" mode. Luciphor will report the scores for each PSM that meets the selection threshold specified for -p. The default output by Luciphor only reports the most confident PSM for each distinct phospho-peptide permutation along with the number of PSMs supporting that permutation. By using this option all PSMs are reported.
--Ascore --Ascore This option executes our version of the Ascore algorithm described in Beausoleil et al. (2006) Nature Biotechnology. This implementation was based upon the published description of the algorithm in that citation. Our implementation differs in that it provides a peptide-level score rather than a site-level score.
-c -c Using this option tells Luciphor to use the nearest modeled charge state to score unmodeled, higher charge state PSMs. Luciphor needs a minimum number of PSMs for each charge state in order to construct accurate predictive models. On occasion, the higher charge states lack sufficient data for accurate modeling. Luciphor's default behavior is to simply not model/score these charge states.
-Z -Z 2 Only model and score PSMs that have the charge state specified after the -Z option.
-o -o results.tsv Custom output file name. The default output filename is based upon the value given to the-i option
-T -T 4 How many CPU threads to use. The maximum value is determined by you specific hardware.
--single --single This option will represent variable modificaitons as lower case characters. By default, Luciphor reports variable modifications as they are shown in the TPP (example: S[167]). Decoy modifications will also be represented by non-alphabetic charaters such as !@#$%&* and numbers.
--hcd --hcd This option activates the higher energy collisional dissociation (HCD) algorithm in Luciphor. The default algorithm is intended for use with CID data.
-t -t 1 Luciphor can generate tab-delimited text files of the spectra for the PSMs it has scored. These files will contain the m/z values, intensity values, and matched fragment ions in that spectra (if any). For each matched fragment ion, you also get the absolute distance of the observed peak to the fragment ion's theoretical m/z value. You also get the intensity and distance score components for each matched peak along with the value that that peak contributes to the final score. The output can either be made with the raw intensity data or the intensities scaled to a range of 0-100.
-N -N By default precursor neutral loss peaks (which are generally very intense for S/T phospho peptides) are removed from the spectrum prior to scoring. Using this option disables this processing step.
-b -b Luciphor will write out the matched spectra for the top two scoring permutations. This output is similar to the one generated by the -t option described above. It differs in that the first column of the output file is a 0 or a 1 indicating which permutation the reported data represents. Note that the entire spectrum will be reported twice in these output files: once for each of the two permutations. Spectra in these files have their intensities scaled to be between 0-100.
-Sl -Sl some_PSMs.txt This option makes Luciphor only report results for the PSMs listed in the given text file. One PSM identifier per line. Lines starting with a '#' character are ignored. You can use this option if you only want to score certain PSMs in your data. Note: This option has no effect on the model parameter estimation part of the algorithm.
-S -S Perform site-level scoring using Luciphor's algorithm (CID or HCD as specified). You will get a likelihood score for each candidate residue in the top-scoring permutation. The syntax will be: residue_position=score. The higher the number, the more likely it is to be phosphorylated. Note: The FLR cannot be estimated using this method.
--noDecoys --noDecoys By default, decoy phospho-permutations are constructed for each scored PSM. This flag disables the false localization rate (FLR) estimation component of the program. By using this option, you will not get any estimate for the false localization rate for your data.
Advanced options
-k -k 1300 Some PSMs are very long and contain many phospho modifications. As such, they require a lot of time to score because of the number of permutations they have. This option lets you restrict which PSMs get scored based upon their permutation complexity. You should only use this option if your Luciphor runs seem to "hang" for a very long time. Likewise, if you want to capture every single phospho-peptide you can increase this value beyond the default of 16384. Note: increasing this parameter beyond the 16384 requires a lot of computer memory.
-n -n 2 By default, all neutral loss peaks (-NH3, -H2O, -H3PO4) are considered by Luciphor for both modeling and scoring. Using this option you can change how they are utilized in the algorithm. The available options are:
1: Do not use neutral loss peaks at all
2: Use them only to obtain the modeling parameters and disregard them when scoring
3: Only consider neutral loss peaks in the final scoring step
--SDI --SDI When performing the final scoring step between the top two candidate permutations, only use site determining ions (SDIs). SDIs are the fragment ions that can be used to distinguish between the two candidate permutations of a PSM. In practice, this option rarely proves useful.
--debug --debug 2 This option makes Luciphor run in debug mode. You use this option to track down problems in the algorithm. You must specify a number from 1 to 6 for debug mode. This determines what debugging output file(s) will be generated.i These can be quite large for complex experiments. In addition, debug mode is restricted to using a single thread for execution. This flag is here for software developers who want to tinker with the code.
  • 1 = Print to the screen each permutation and it's score for each PSM
  • 2 = Write to disk a file called ionScores.debug which reports the ions that were scored by Luciphor along with the scores these ions received.
  • 3 = Write to disk a file called modelData.debug which reports the ions that were used by Luciphor for model parameter estimations
  • 4 = Write to disk a file called mzErrWinMatched.txt which reports the the distances of candidate matched peaks in within the m/z window specified by the user.
  • 5 = Write to disk two files called density_intensity.txt and density_distance.txt which report the data used for the estimation of the non-parametric model in HCD mode.
  • 6 = Write to disk a file called peak_data.debug which can be used to debug the Ascore results produced by Luciphor