Commit d993424c authored by Till Bald's avatar Till Bald

Update OPTIONS.MD

parent d03693e1
Pipeline #6754330 passed with stages
in 104 minutes and 40 seconds
......@@ -4,148 +4,138 @@ 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.
* `-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.
* `-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
* `-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.
* `-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.
* `-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.
* `-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
* `-minPeptideLength <int>` (default: 5)
Minimum peptide length
-18O <flag> (default: false)
digestion with 18O water, labelling of c terminus (+ 2.004 Da.)
* `-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.
* `-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.
* `-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 "_"
* `-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
* `-ionsToSearch <a, b, c, x, y, z>` (default: b,y)
Ions to search
-calculateLosses <flag> (default: false)
Ions to search
* `-calculateLosses <flag>` (default: false)
Calculate neutral losses
MS2 handling
------------
-deconvolution <flag> (default: true)
Deconvolution (determince uncharged masses from m/z values)
* `-deconvolution <flag>` (default: true)
Deconvolution (determince uncharged masses from m/z values)
-removeNoise <flag> (default: true)
Remove noise from spectrum
* `-removeNoise <flag>` (default: true)
Remove noise from spectrum
Scoring
-------
-minimumMatches <int> (default: 6)
Minimum matching peaks (spectrum)
* `-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)
* `-maxIsotopeNumber <int>` (default: 0)
maximum isotope number that is allowed in MS1 scans. (0 = monoisotopic)
-MS2Isotope <string> (default: monoisotopic)
Product ion (MS2) search type.
* `-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.
* `-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_decoy <string>` (default: `__td__decoy_`)
Specify prefix for decoy sequence identifiers.
-td_prefix_target <string> (default: __td__target_)
Specify prefix for target 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!
* `-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
* `-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
* `-outputDirectory <string>` (default: )
Output directory
-outputPrefix <string> (default: )
Output file prefix
* `-outputPrefix <string>` (default: )
Output file prefix
-outputWriteIdentified_crosslinks_perScan <flag> (default: yes)
Write identified cross-linked PSM (crosslinx-results.csv)
* `-outputWriteIdentified_crosslinks_perScan <flag>` (default: yes)
Write identified cross-linked PSM (crosslinx-results.csv)
Input files
-----------
- at least 1 protein database A file
- at least 1 protein database A file
format: FASTA (.fasta|.fas|.fa|.faa|.fna|.ffn|.frn)
- at least 1 protein database B file
- at least 1 protein database B file
format: FASTA (.fasta|.fas|.fa|.faa|.fna|.ffn|.frn)
- at least 1 mzML file
- at least 1 mzML file
format: mzML (.mzml), mzML (compressed) (.mzml.zip|.mzml.gz|.mzml.bz2)
- at least 0 PSM files
- at least 0 PSM files
format: Comma separated values (.csv)
- at least 0 cross-linked PSM files
- at least 0 cross-linked PSM files
format: Comma separated values (.csv)
......@@ -165,15 +155,19 @@ Affected input file formats:
Input file group assignment switches:
-fastaFilesA: subsequent files are interpreted as protein database A
* `-fastaFilesA`:
subsequent files are interpreted as protein database A
files
-fastaFilesB: subsequent files are interpreted as protein database B
* `-fastaFilesB`:
subsequent files are interpreted as protein database B
files
-omssaFiles: subsequent files are interpreted as PSM files
* `-omssaFiles`:
subsequent files are interpreted as PSM files
-crosslinkFiles: subsequent files are interpreted as cross-linked PSM
* `-crosslinkFiles`:
subsequent files are interpreted as cross-linked PSM
files
Output directory
......
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