OPTIONS.MD 4.82 KB
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Please refer to the [readme](https://gitlab.com/bald/Crosslinx/blob/master/README.md) for a more general help. 
This pages lists all options that are available in Crosslinx.

Masses and tolerance
--------------------

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* `-ppmMS1 <float>` (default: 5.0)   
Specify the mass accuracy for identifying precursor ions of crosslinked peptides in MS1 spectra.
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* `-ppmMS2 <float>` (default: 20.0)  
Specify the mass accuracy for assigning in silico fragmented peptides to MS2 spectra.
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* `-cShift <flag>` (default: false)     
All cysteines in a sequence are considered as having the modification
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Enzyme specification
--------------------

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* `-enzyme <string>` (default: Trypsin (RK|))  
Specify the enzyme used for in silico digestion of the protein database.
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* `-notCleavedAminoAcids <string>` (default: Trypsin (P))  
Specify the amino acids before a cleavage site, after which the enzyme does not cut.
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* `-missedCleavageSites <int>` (default: 3)   
Specify the number of missed cleavages for in silico digestion of the protein database.
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* `-minPeptideLength <int>` (default: 5)   
Minimum peptide length
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* `-18O <flag>` (default: false)   
digestion with 18O water, labelling of c terminus (+ 2.004 Da.)
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Cross-linker specification
--------------------------

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* `-crossLinkerMass <string>` (default: 138.0680796 (DSSd0))    
Enter the mass here, optionally followed by a space and some descriptive text.
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* `-crossLinkerMassShift <string>` (default: 4.025107 (d0/d4))   
Enter the mass shift here, optionally followed by a space and some descriptive text.
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* `-crosslinkedAA <string>` (default: K (DSS and BS3))   
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Enter the amino acids which are crosslinked, optionally followed by a space and some descriptive text. N-terminus indicated by "_"
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Ions to search
--------------

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* `-ionsToSearch <a, b, c, x, y, z>` (default: b,y)   
Ions to search
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* `-calculateLosses <flag>` (default: false)   
Calculate neutral losses
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MS2 handling
------------

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* `-deconvolution <flag>` (default: true)   
Deconvolution (determince uncharged masses from m/z values)
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* `-removeNoise <flag>` (default: true)
Remove noise from spectrum
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Scoring
-------

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* `-minimumMatches <int>` (default: 6)   
Minimum matching peaks (spectrum)
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Isotopic distribution
---------------------

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* `-maxIsotopeNumber <int>` (default: 0)   
maximum isotope number that is allowed in MS1 scans. (0 = monoisotopic)
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* `-MS2Isotope <string>` (default: monoisotopic)   
Product ion (MS2) search type.
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target/decoy
------------

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* `-decoy_on_demand <flag>` (default: false)   
Build decoy peptides (reverse, keep end) on demand for every target
combination that matches in MS1 scans. No target/decoy database is required.
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* `-td_prefix_decoy <string>` (default: `__td__decoy_`)   
Specify prefix for decoy sequence identifiers.
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* `-td_prefix_target <string>` (default: `__td__target_`)   
Specify prefix for target sequence identifiers.
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Tweaks
------

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* `-cache <flag>` (default: false)   
Use caching for MS2 fragment ions. Should be used with small protein
databases on high number of spectra. Enabling this option when using a
large database may use VERY much RAM!
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Output
------

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* `-plot <flag>` (default: false)   
Creates a plot for every MS2 scan with hits including the
corresponding MS1 scan. Plots are stored in the output directory
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Output files
------------

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* `-outputDirectory <string>` (default: )   
Output directory
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* `-outputPrefix <string>` (default: )   
Output file prefix
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* `-outputWriteIdentified_crosslinks_perScan <flag>` (default: yes)   
Write identified cross-linked PSM (crosslinx-results.csv)
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Input files
-----------

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- at least 1 protein database A file   
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  format: FASTA (.fasta|.fas|.fa|.faa|.fna|.ffn|.frn)


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- at least 1 protein database B file   
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  format: FASTA (.fasta|.fas|.fa|.faa|.fna|.ffn|.frn)


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- at least 1 mzML file   
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  format: mzML (.mzml), mzML (compressed) (.mzml.zip|.mzml.gz|.mzml.bz2)


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- at least 0 PSM files   
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  format: Comma separated values (.csv)


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- at least 0 cross-linked PSM files   
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  format: Comma separated values (.csv)


Input file ambiguities
----------------------

Because some input file formats appear in multiple input file groups,
files in some input formats must be manually assigned to a certain
input file group by preceding the filenames with the appropriate
switches.

Affected input file formats:

- Comma separated values (.csv)

- FASTA (.fasta|.fas|.fa|.faa|.fna|.ffn|.frn)

Input file group assignment switches:

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* `-fastaFilesA`:   
subsequent files are interpreted as protein database A
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files

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* `-fastaFilesB`:   
subsequent files are interpreted as protein database B
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files

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* `-omssaFiles`:   
subsequent files are interpreted as PSM files
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* `-crosslinkFiles`:   
subsequent files are interpreted as cross-linked PSM
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files

Output directory
----------------

Unless an output directory is specified, the output files will be
written to the directory of the first mzML file.