OPTIONS.MD 4.75 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
--------------------

-ppmMS1 <float> (default: 5.0)
    Specify the mass accuracy for identifying precursor ions of
    crosslinked peptides in MS1 spectra.

-ppmMS2 <float> (default: 20.0)
    Specify the mass accuracy for assigning in silico fragmented peptides
    to MS2 spectra.

-cShift <flag> (default: false)
    All cysteines in a sequence are considered as having the modification

Enzyme specification
--------------------

-enzyme <string> (default: Trypsin (RK|))
    Specify the enzyme used for in silico digestion of the protein
    database.

-notCleavedAminoAcids <string> (default: Trypsin (P))
    Specify the amino acids before a cleavage site, after which the enzyme
    does not cut.

-missedCleavageSites <int> (default: 3)
    Specify the number of missed cleavages for in silico digestion of the
    protein database.

-minPeptideLength <int> (default: 5)
    Minimum peptide length

-18O <flag> (default: false)
    digestion with 18O water, labelling of c terminus (+ 2.004 Da.)

Cross-linker specification
--------------------------

-crossLinkerMass <string> (default: 138.0680796 (DSSd0))
    Enter the mass here, optionally followed by a space and some
    descriptive text.

-crossLinkerMassShift <string> (default: 4.025107 (d0/d4))
    Enter the mass shift here, optionally followed by a space and some
    descriptive text.

-crosslinkedAA <string> (default: K (DSS and BS3))
    Enter the amino acids which are crosslinked, optionally followed by a
    space and some descriptive text. N-terminus indicated by "_"

Ions to search
--------------

-ionsToSearch <a, b, c, x, y, z> (default: b,y)
    Ions to search

-calculateLosses <flag> (default: false)
    Ions to search

MS2 handling
------------

-deconvolution <flag> (default: true)
    Deconvolution (determince uncharged masses from m/z values)

-removeNoise <flag> (default: true)
    Remove noise from spectrum

Scoring
-------

-minimumMatches <int> (default: 6)
    Minimum matching peaks (spectrum)

Isotopic distribution
---------------------

-maxIsotopeNumber <int> (default: 0)
    maximum isotope number that is allowed in MS1 scans. (0 =
    monoisotopic)

-MS2Isotope <string> (default: monoisotopic)
    Product ion (MS2) search type.

target/decoy
------------

-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.

-td_prefix_decoy <string> (default: __td__decoy_)
    Specify prefix for decoy sequence identifiers.

-td_prefix_target <string> (default: __td__target_)
    Specify prefix for target sequence identifiers.

Tweaks
------

-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!

Output
------

-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

Output files
------------

-outputDirectory <string> (default: )
    Output directory

-outputPrefix <string> (default: )
    Output file prefix

-outputWriteIdentified_crosslinks_perScan <flag> (default: yes)
    Write identified cross-linked PSM (crosslinx-results.csv)

Input files
-----------

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


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


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


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


- at least 0 cross-linked PSM files
  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:

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

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

-omssaFiles: subsequent files are interpreted as PSM files

-crosslinkFiles: subsequent files are interpreted as cross-linked PSM
files

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

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