Commit d03693e1 authored by Till Bald's avatar Till Bald

[help] initial commit of options.md

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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.
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