"C:\Program Files\sirius\sirius" project-space --help
Commands:
config <CONFIGURATION> Override all possible default
configurations of this toolbox from the
command line.
project-space, PS <STANDALONE> Modify a given project Space:
Read project(s) with --input, apply
modification and write the result via
--output. If either --input or --output is
given, the modifications will be made
in-place.
custom-db, DB
<STANDALONE> Generate a custom searchable
structure database. Import multiple files
with compounds as SMILES or InChi into this
DB.
similarity <STANDALONE> Computes the similarity between
all compounds in the dataset and outputs a
matrix of similarities.
decomp <STANDALONE> Small tool to decompose masses
with given deviation, ionization, chemical
alphabet and chemical filter.
mgf-export, MGF <STANDALONE> Exports the spectra of a given
input as mgf.
ftree-export <STANDALONE> Exports the fragmentation trees
of a project into various formats
prediction-export, EPR <STANDALONE> Exports predictions from CSI:
FingerID and CANOPUS.
fingerprinter, FP Compute SIRIUS compatible fingerprints from
PubChem standardized SMILES in tsv format.
gui, GUI Starts the graphical user interface of SIRIUS
asService, rest, REST EXPERIMENTAL/UNSTABLE: Starts SIRIUS as a
background (REST) service that can be
requested via a REST-API
login <STANDALONE> Allows a user to login for
SIRIUS Webservices (e.g. CSI:FingerID or
CANOPUS) and securely store a personal
access token.
settings <STANDALONE> Configure persistent (technical)
settings of SIRIUS (e.g. ProxySettings or
ILP Solver).
install-autocompletion <INSTALL> generates and installs an
Autocompletion-Script with all subcommands.
Default installation is for the current user
write-summaries, W <STANDALONE, POSTPROCESSING> Write Summary
files from a given project-space into the
given project-space or a custom location.
lcms-align, A <PREPROCESSING> Align and merge compounds of
multiple LCMS Runs. Use this tool if you
want to import from mzML/mzXml
zodiac, rerank-formulas <DATASET_TOOL> Identify Molecular formulas of
all compounds in a dataset together using
ZODIAC.
formula, tree, sirius <COMPOUND_TOOL> Identify molecular formula
for each compound individually using
fragmentation trees and isotope patterns.
fingerprint <COMPOUND_TOOL> Predict molecular fingerprint
from MS/MS and fragmentation trees for each
compound Individually using CSI:FingerID
fingerprint prediction.
structure, search-structure-db <COMPOUND_TOOL> Search in molecular structure
db for each compound Individually using CSI:
FingerID structure database search.
passatutto <COMPOUND_TOOL> Compute a decoy spectra based
on the fragmentation trees of the given
input spectra. If no molecular formula is
provided in the input, the top scoring
computed formula is used.
canopus, compound-classes <COMPOUND_TOOL> Predict compound categories
for each compound individually based on its
predicted molecular fingerprint (CSI:
FingerID) using CANOPUS.
"C:\Program Files\sirius\sirius" canopus --help
Usage: sirius canopus [-hV] [COMMAND]
<COMPOUND_TOOL> Predict compound categories for each compound individually
based on its predicted molecular fingerprint (CSI:FingerID) using CANOPUS.
-h, --help Show this help message and exit.
-V, --version Print version information and exit.
Commands:
write-summaries, W <STANDALONE, POSTPROCESSING> Write Summary files from a
given project-space into the given project-space or a
custom location.
"C:\Program Files\sirius\sirius" passatutto --help
Usage: sirius passatutto [-hV] [COMMAND]
<COMPOUND_TOOL> Compute a decoy spectra based on the fragmentation trees of the
given input spectra. If no molecular formula is provided in the input, the top
scoring computed formula is used.
-h, --help Show this help message and exit.
-V, --version Print version information and exit.
Commands:
fingerprint <COMPOUND_TOOL> Predict molecular fingerprint from MS/MS
and fragmentation trees for each compound Individually
using CSI:FingerID fingerprint prediction.
write-summaries, W <STANDALONE, POSTPROCESSING> Write Summary files from a
given project-space into the given project-space or a
custom location.
"C:\Program Files\sirius\sirius" structure --help
Usage: sirius structure [-hV] [-d=<dbName>[,<dbName>...]]
[-l=<injectElGordoCompounds>] [COMMAND]
<COMPOUND_TOOL> Search in molecular structure db for each compound Individually
using CSI:FingerID structure database search.
-d, --db, --database=<dbName>[,<dbName>...]
Search structure in the union of the given databases. If no
database is given the default database(s) are used.
Example: possible DBs: 'ALL,ALL_BUT_INSILICO,BIO,PUBCHEM,MESH,
HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,
ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,
PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,
PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,
KEGGMINE,ECOCYCMINE,YMDBMINE'
Default: BIO
-h, --help Show this help message and exit.
-l, --elgordo, tag-lipids, flag-lipids=<injectElGordoCompounds>
Tag candidates that are matching lipid class determined by El
Gordo in CSI:FingerID candidate list.
Default: True
-V, --version Print version information and exit.
Commands:
canopus, compound-classes <COMPOUND_TOOL> Predict compound categories for
each compound individually based on its
predicted molecular fingerprint (CSI:FingerID)
using CANOPUS.
write-summaries, W <STANDALONE, POSTPROCESSING> Write Summary files
from a given project-space into the given
project-space or a custom location.
"C:\Program Files\sirius\sirius" fingerprint --help
Usage: sirius fingerprint [-hV] [--no-threshold] [COMMAND]
<COMPOUND_TOOL> Predict molecular fingerprint from MS/MS and fragmentation
trees for each compound Individually using CSI:FingerID fingerprint prediction.
-h, --help Show this help message and exit.
--no-threshold Disable score threshold for formula candidates. CSI:
FingerID fingerprints will be predicted for all
formula candidates
-V, --version Print version information and exit.
Commands:
structure, search-structure-db <COMPOUND_TOOL> Search in molecular structure
db for each compound Individually using CSI:
FingerID structure database search.
canopus, compound-classes <COMPOUND_TOOL> Predict compound categories
for each compound individually based on its
predicted molecular fingerprint (CSI:
FingerID) using CANOPUS.
write-summaries, W <STANDALONE, POSTPROCESSING> Write Summary
files from a given project-space into the
given project-space or a custom location.
"C:\Program Files\sirius\sirius" zodiac --help
Usage: sirius zodiac [-hV] [--ignore-spectra-quality] [--burn-in=<burnInSteps>]
[--considered-candidates-at-300=<numberOfConsideredCandidat
esBelow300>]
[--considered-candidates-at-800=<numberOfConsideredCandidat
esAbove800>] [--iterations=<iterationSteps>]
[--lambda=<lambda>] [--library-hits=<libraryHits>]
[--min-cosine=<minCosine>]
[--minLocalConnections=<minLocalConnections>]
[--thresholdFilter=<thresholdFilter>] [COMMAND]
<DATASET_TOOL> Identify Molecular formulas of all compounds in a dataset
together using ZODIAC.
--burn-in=<burnInSteps>
Number of epochs considered as 'burn-in period'.
Default: 2000
--considered-candidates-at-300=<numberOfConsideredCandidatesBelow300>
Maximum number of candidate molecular formulas
(fragmentation trees computed by SIRIUS) per
compound which are considered by ZODIAC for
compounds below 300 m/z.
Default: 10
--considered-candidates-at-800=<numberOfConsideredCandidatesAbove800>
Maximum number of candidate molecular formulas
(fragmentation trees computed by SIRIUS) per
compound which are considered by ZODIAC for
compounds above 800 m/z.
Default: 50
-h, --help Show this help message and exit.
--ignore-spectra-quality
As default ZODIAC runs a 2-step approach. First
running 'good quality compounds' only, and
afterwards including the remaining.
--iterations=<iterationSteps>
Number of epochs to run the Gibbs sampling. When
multiple Markov chains are computed, all chains'
iterations sum up to this value.
Default: 20000
--lambda=<lambda> Lambda used in the scoring function of spectral
library hits. The higher this value the higher are
library hits weighted in ZODIAC scoring.
Default: 1000
--library-hits=<libraryHits>
CSV file containing spectral library hits. Library
hits are used as anchors to improve ZODIAC scoring.
--min-cosine=<minCosine>
Spectral library hits must have at least this cosine
or higher to be considered in scoring.
Value must be in [0,1].
Default: 0.5
--minLocalConnections=<minLocalConnections>
Minimum number of compounds to which at least one
candidate per compound must be connected to.
Default: 10
--thresholdFilter=<thresholdFilter>
Defines the proportion of edges of the complete
network which will be ignored.
Default: 0.95
-V, --version Print version information and exit.
Commands:
passatutto <COMPOUND_TOOL> Compute a decoy spectra based on the
fragmentation trees of the given input spectra. If no
molecular formula is provided in the input, the top
scoring computed formula is used.
fingerprint <COMPOUND_TOOL> Predict molecular fingerprint from MS/MS
and fragmentation trees for each compound Individually
using CSI:FingerID fingerprint prediction.
write-summaries, W <STANDALONE, POSTPROCESSING> Write Summary files from a
given project-space into the given project-space or a
custom location.
"C:\Program Files\sirius\sirius" write-summaries --help
Usage: sirius write-summaries [-chV] [--[no-]full-summary] [--[no-]
top-hit-summary] [--[no-]top-hit-adduct-summary]
[-o=<location>] [[--classyfire] [--npc]
[--fingerprint] [--pubchem] [--maccs] [--all]
[-p=<digits>]]
<STANDALONE, POSTPROCESSING> Write Summary files from a given project-space
into the given project-space or a custom location.
-c, --zip, --compress Summaries will be written into a compressed zip
archive. This parameter will be ignored if the
summary is written into the project-space.
--[no-]full-summary Write project wide summary files with ALL Hits.
(Use with care! Might create large files and
consume large amounts of memory for large
projects.)
-h, --help Show this help message and exit.
--[no-]top-hit-summary
Write project wide summary files with all Top Hits.
-o, --output=<location> Specify location (outside the project) for writing
summary files. Per default summaries are written
to the project-space
--[no-]top-hit-adduct-summary
Write project wide summary files with all Top Hits
and their adducts
-V, --version Print version information and exit.
Include Predictions Table --all Output all predicted CSI:FingerID and CANOPUS
probabilities (sets --fingerprints, --classyfire,
--npc).
--classyfire Output predicted classyfire probabilities by
CANOPUS.
--fingerprint, --fingerprints
Output predicted fingerprint probabilities by CSI:
FingerID.
--maccs Output predicted MACCS fingerprint probabilities by
CSI:FingerID (subset of --fingerprint).
--npc Output predicted NPC (natural product classifier)
probabilities by CANOPUS.
-p, --digits, --precision=<digits>
Specify number of digits used for printing floating
point values. -1 -> full length Double value.
Default: -1
--pubchem Output predicted PubChem fingerprint probabilities
"C:\Program Files\sirius\sirius" install-autocompletion --help
Usage: sirius install-autocompletion [-hiuV] [-l=<scriptFile>]
[-n=<siriusName>] [-o=<OS>] [[-g] | [-c]]
<INSTALL> generates and installs an Autocompletion-Script with all subcommands.
Default installation is for the current user
-c, --cancelinstall does not install the Completionscript
-g, --global installs the Completionscript globally into
/etc/bash-completion.d (requires root permission
and [bash-completion] (https://github.
com/scop/bash-completion))
-h, --help Show this help message and exit.
-i, --ignore-version ignores the version check while uninstalling the
AutocompletionScript
-l, --location=<scriptFile>
Target directory to store the script file. DEFAULT
is the current working directory. Directory must
exist.
-n, --name=<siriusName> Alternative name for the sirius Application
-o, --OStype=<OS> Overrides specification of the SystemOS. (Detected
automatically per Default) Possibilities: {Linux,
Mac, Solaris}
-u, --uninstall uninstalls the completionScript. Please add -g for
global uninstallation
-V, --version Print version information and exit.
"C:\Program Files\sirius\sirius" settings --help
Usage: sirius settings [-hV] [-k=<key> -v=<value>]... [--proxy
--host=<hostname> --port=<port> [--user=<user>
--pw=<password>]]
<STANDALONE> Configure persistent (technical) settings of SIRIUS (e.g.
ProxySettings or ILP Solver).
-h, --help Show this help message and exit.
-V, --version Print version information and exit.
Generic key-value pairs of properties.
-k, --key=<key> Property Key
-v, --value=<value> Property Value
Properties to configure Proxy server for SIRIUS.
--host=<hostname> Proxy domain.
--port=<port> Proxy port.
--proxy Define proxy settings.
--pw, --password=<password>
Proxy password (only if proxy server needs
credentials.
--user=<user> Proxy user (only if proxy server needs credentials.
"C:\Program Files\sirius\sirius" prediction-export --help
Usage: sirius prediction-export [-hV] [-c=<polarity>] [-o=<output>]
[[--classyfire] [--npc] [--fingerprint]
[--pubchem] [--maccs] [--all] [-p=<digits>]]
<STANDALONE> Exports predictions from CSI:FingerID and CANOPUS.
-c, --charge, --polarity=<polarity>
Restrict output to the given polarity. By default
this value is 0 and the polarity of the first
compound in the project space is chosen. Note that
each output file can only contain predictions from
one polarity.
--classyfire Output predicted classyfire probabilities by CANOPUS.
--npc Output predicted NPC (natural product classifier)
probabilities by CANOPUS.
--fingerprint, --fingerprints
Output predicted fingerprint probabilities by CSI:
FingerID.
--pubchem Output predicted PubChem fingerprint probabilities by
CSI:FingerID (subset of --fingerprint).
--maccs Output predicted MACCS fingerprint probabilities by
CSI:FingerID (subset of --fingerprint).
--all Output all predicted CSI:FingerID and CANOPUS
probabilities (sets --fingerprints, --classyfire,
--npc).
-p, --digits, --precision=<digits>
Specify number of digits used for printing floating
point values. -1 -> full length Double value.
-o, --output=<output> Specify the table file destination.
-h, --help Show this help message and exit.
-V, --version Print version information and exit.
"C:\Program Files\sirius\sirius" project-space --help
Usage: sirius project-space [-hmV] [--dm=<makeDeleteMassFilter>]
[--dn=<makeDeleteIdxFilter>]
[--kc=<makeKeepConfidenceFilter>]
[--kei=<makeKeepExplainedIntensityFilter>]
[--km=<makeKeepMassFilter>]
[--kn=<makeKeepNameFilter>]
[--kts=<makeKeepTreeSizeFilter>]
[--merge-compounds-cosine=<mergeCompoundsCosine>]
[--merge-compounds-rtdiff=<mergeCompoundsRtDiff>]
[--merge-compounds-top=<mergeCompoundsTopK>]
[-d=<makeDeleteIdxFilter>[,
<makeDeleteIdxFilter>...]]...
[-k=<makeKeepIdxFilter>[,
<makeKeepIdxFilter>...]]... [[-s=<type>]
[-c=<count>] [-o=<order>]]
<STANDALONE> Modify a given project Space: Read project(s) with --input, apply
modification and write the result via --output. If either --input or --output
is given, the modifications will be made in-place.
-d, --di, --delete-by-idx=<makeDeleteIdxFilter>[,<makeDeleteIdxFilter>...]
Delete all compounds that match the given indices from
the given project-space.
--dm, --delete-by-mass=<makeDeleteMassFilter>
Delete all compounds that are within the given mass
window.
Example: Use 'mass1:mass2' to match compounds with
mass1 <= mass <= mass2. Leave a value empty to set no
bound.
--dn, --delete-by-name=<makeDeleteIdxFilter>
Delete all compounds where the 'identifier' (dir name,
ID) matches the given regex (JAVA).
-h, --help Show this help message and exit.
-k, --ki, --keep-by-idx=<makeKeepIdxFilter>[,<makeKeepIdxFilter>...]
Keep all compounds that match the given indices from
the given project-space
--kc, --keep-by-confidence=<makeKeepConfidenceFilter>
Keep all compounds that have a valid confidence score
greater or equal than the given minimum confidence.
--kei, --keep-by-explained-intensity=<makeKeepExplainedIntensityFilter>
Keep all compounds that have at least one fragmentation
tree that explains at least a minimum total intensity
of the spectrum. Value between 0 to 1.
--km, --keep-by-mass=<makeKeepMassFilter>
Keep all compounds that are within the given mass
window.
Example: Use 'mass1:mass2' to match compounds with
mass1 <= mass <= mass2. Leave a value empty to set no
bound.
--kn, --keep-by-name=<makeKeepNameFilter>
Keep all compounds where the 'identifier' (Dir name,
ID) matches the given regex (JAVA).
--kts, --keep-by-tree-size=<makeKeepTreeSizeFilter>
Keep all compounds that have at least one fragmentation
tree with number of fragments (including precursor)
greater or equal than the given minimum.
-m, --move DANGERZONE: Move instead of copy data (where possible)
when merging or splitting projects to save time. Be
aware of the risk that you may end up with corrupted
input or output data when the program crashes.
--merge-compounds-cosine=<mergeCompoundsCosine>
Merge compounds which have the same spectra and m/z
into one. The criteria for merging can be specified
with --merge-compounds-cosine and
--merge-compounds-rtdiff.
--merge-compounds-rtdiff=<mergeCompoundsRtDiff>
Merge compounds which have the same spectra and m/z
into one. The criteria for merging can be specified
with --merge-compounds-cosine and
--merge-compounds-rtdiff. Retention time difference
for merging is either specified in seconds, or by
adding a unit after the number (e.g., '5 min'
--merge-compounds-top=<mergeCompoundsTopK>
Merge compounds which have the same spectra and m/z
into one. For each such cluster of compounds, keep
only the top k most abundant ones. The criteria for
merging can be specified with
--merge-compounds-cosine and --merge-compounds-rtdiff.
-V, --version Print version information and exit.
Split the project into chunks:
-c, --count=<count> Sets batch number or batch size depending on <--split>
Default: 1
-o, --split-order=<order>
Specify the order of Compounds before putting them into
batches.
Default: SHUFFLE
-s, --split=<type> Split the output into batches. Either in a specific
number of batches or in batches of specific size!
Default: NO
"C:\Program Files\sirius\sirius" config --help
情報: Running with following arguments: [config, --help]
Usage: sirius config [-hV] [--AdductSettings.detectable=[M+H]+,[M+K]+,[M+Na]+,
[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,
[M+Br]-] [--AdductSettings.enforced=,] [--AdductSettings.
fallback=[M+H]+,[M-H]-,[M+Na]+,[M+K]+]
[--AlgorithmProfile=default] [--CandidateFormulas=,]
[--CompoundQuality=UNKNOWN]
[--ForbidRecalibration=ALLOWED]
[--FormulaResultRankingScore=AUTO]
[--FormulaResultThreshold=true] [--FormulaSearchDB=none]
[--FormulaSettings.detectable=S,Br,Cl,B,Se]
[--FormulaSettings.enforced=C,H,N,O,P] [--FormulaSettings.
fallback=S] [--InjectElGordoCompounds=True]
[--IsotopeMs2Settings=IGNORE] [--IsotopeSettings.
filter=True] [--IsotopeSettings.multiplier=1]
[--MedianNoiseIntensity=0.015] [--MotifDbFile=none] [--ms1.
absoluteIntensityError=0.02] [--ms1.
minimalIntensityToConsider=0.01] [--ms1.
relativeIntensityError=0.08] [--MS1MassDeviation.
allowedMassDeviation=10.0 ppm] [--MS1MassDeviation.
massDifferenceDeviation=5.0 ppm] [--MS1MassDeviation.
standardMassDeviation=10.0 ppm] [--MS2MassDeviation.
allowedMassDeviation=10.0 ppm] [--MS2MassDeviation.
standardMassDeviation=10.0 ppm] [--NoiseThresholdSettings.
absoluteThreshold=0] [--NoiseThresholdSettings.
basePeak=NOT_PRECURSOR] [--NoiseThresholdSettings.
intensityThreshold=0.005] [--NoiseThresholdSettings.
maximalNumberOfPeaks=60] [--NumberOfCandidates=10]
[--NumberOfCandidatesPerIon=1]
[--NumberOfStructureCandidates=10000]
[--PossibleAdductSwitches=[M+Na]+:[M+H]+,[M+K]+:[M+H]+,
[M+Cl]-:[M-H]-] [--PrintCitations=True]
[--RecomputeResults=False]
[--StructurePredictors=CSI_FINGERID]
[--StructureSearchDB=BIO] [--Timeout.secondsPerInstance=0]
[--Timeout.secondsPerTree=0] [--UseHeuristic.
mzToUseHeuristic=300] [--UseHeuristic.
mzToUseHeuristicOnly=650] [--ZodiacClusterCompounds=false]
[--ZodiacEdgeFilterThresholds.minLocalCandidates=1]
[--ZodiacEdgeFilterThresholds.minLocalConnections=10]
[--ZodiacEdgeFilterThresholds.thresholdFilter=0.95]
[--ZodiacEpochs.burnInPeriod=2000] [--ZodiacEpochs.
iterations=20000] [--ZodiacEpochs.numberOfMarkovChains=10]
[--ZodiacLibraryScoring.lambda=1000]
[--ZodiacLibraryScoring.minCosine=0.5]
[--ZodiacNumberOfConsideredCandidatesAt300Mz=10]
[--ZodiacNumberOfConsideredCandidatesAt800Mz=50]
[--ZodiacRatioOfConsideredCandidatesPerIonization=0.2]
[--ZodiacRunInTwoSteps=true] [COMMAND]
<CONFIGURATION> Override all possible default configurations of this toolbox
from the command line.
--AdductSettings.detectable=[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,
[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-
Detectable ion modes which are only considered if
there is an indication in the MS1 scan (e.g.
correct mass delta).
--AdductSettings.enforced=,
Describes how to deal with Adducts:
Pos Examples:
[M+H]+,[M]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+Na2-H]+,
[M+2K-H]+,[M+NH4]+,[M+H3O]+,[M+MeOH+H]+,[M+ACN+H]+,
[M+2ACN+H]+,[M+IPA+H]+,[M+ACN+Na]+,[M+DMSO+H]+
Neg Examples:
[M-H]-,[M]-,[M+K-2H]-,[M+Cl]-,[M-H2O-H]-,[M+Na-2H]-,
M+FA-H]-,[M+Br]-,[M+HAc-H]-,[M+TFA-H]-,[M+ACN-H]-
Enforced ion modes that are always considered.
--AdductSettings.fallback=[M+H]+,[M-H]-,[M+Na]+,[M+K]+
Fallback ion modes which are considered if the auto
detection did not find any indication for
an ion mode.
--AlgorithmProfile=default
Configuration profile to store instrument specific
algorithm properties.
Some of the default profiles are: 'qtof',
'orbitrap', 'fticr'.
--CandidateFormulas=,
This configuration holds a set of user given
formulas to be used as candidates for SIRIUS
Note: This set might be merged with other sources
like formulas from databases
Set of Molecular Formulas to be used as candidates
for molecular formula estimation with
SIRIUS
--CompoundQuality=UNKNOWN
Keywords that can be assigned to a input spectrum to
judge its quality. Available keywords
are: Good, LowIntensity, NoMS1Peak, FewPeaks,
Chimeric, NotMonoisotopicPeak,
PoorlyExplained
--ForbidRecalibration=ALLOWED
Enable/Disable the hypothesen driven recalibration
of MS/MS spectra
Must be either 'ALLOWED' or FORBIDDEN'
--FormulaResultRankingScore=AUTO
Allows the USER to Specify the ScoreType that is
used to rank the list of Molecular Formula
Identifications
before CSI:FingerID predictions are calculated. Auto
means that this ScoreType is
automatically set depending on the executed workflow.
--FormulaResultThreshold=true
Specifies if the list of Molecular Formula
Identifications is filtered by a soft threshold
(calculateThreshold) before CSI:FingerID predictions
are calculated.
--FormulaSearchDB=none
--FormulaSettings.detectable=S,Br,Cl,B,Se
Detectable elements are added to the chemical
alphabet, if there are indications for them
(e.g. in isotope pattern)
--FormulaSettings.enforced=C,H,N,O,P
These configurations hold the information how to
autodetect elements based on the given
formula constraints.
Note: If the compound is already assigned to a
specific molecular formula, this annotation is
ignored.
Enforced elements are always considered
--FormulaSettings.fallback=S
Fallback elements are used, if the auto-detection
fails (e.g. no isotope pattern available)
-h, --help Show this help message and exit.
--InjectElGordoCompounds=True
Candidates matching the lipid class estimated by El
Gordo will be tagged.
The lipid class will only be available if El Gordo
predicts that the MS/MS is a lipid spectrum.
If this parameter is set to 'false' El Gordo will
still be executed and e.g. improve the
fragmentation
tree, but the matching candidates will not be tagged
as lipid class.
--IsotopeMs2Settings=IGNORE
--IsotopeSettings.filter=True
This configurations define how to deal with isotope
patterns in MS1.
When filtering is enabled, molecular formulas are
excluded if their theoretical isotope
pattern does not match
the theoretical one, even if their MS/MS pattern has
high score.
--IsotopeSettings.multiplier=1
multiplier for the isotope score. Set to 0 to
disable isotope scoring. Otherwise, the score
from isotope
pattern analysis is multiplied with this
coefficient. Set to a value larger than one if
your
isotope
pattern data is of much better quality than your
MS/MS data.
--MedianNoiseIntensity=0.015
--MotifDbFile=none
--ms1.absoluteIntensityError=0.02
The average absolute deviation between theoretical
and measured intensity of isotope
peaks.
Do not change this parameter without a good reason!
--ms1.minimalIntensityToConsider=0.01
Ignore isotope peaks below this intensity.
This value should reflect the smallest relative
intensive which is still above noise level.
Obviously, this is hard to judge without having
absolute values. Keeping this value around 1
percent is
fine for most settings. Set it to smaller values if
you trust your small intensities.
--ms1.relativeIntensityError=0.08
The average relative deviation between theoretical
and measured intensity of isotope
peaks.
Do not change this parameter without a good reason!
--MS1MassDeviation.allowedMassDeviation=10.0 ppm
Mass accuracy setting for MS1 spectra. Mass
accuracies are always written as "X ppm (Y Da)"
with X and Y
are numerical values. The ppm is a relative measure
(parts per million), Da is an absolute
measure. For each mass, the
maximum of relative and absolute is used.
--MS1MassDeviation.massDifferenceDeviation=5.0 ppm
--MS1MassDeviation.standardMassDeviation=10.0 ppm
--MS2MassDeviation.allowedMassDeviation=10.0 ppm
Mass accuracy setting for MS2 spectra. Mass
Accuracies are always written as "X ppm (Y Da)"
with X and Y
are numerical values. The ppm is a relative measure
(parts per million), Da is an absolute
measure. For each mass, the
maximum of relative and absolute is used.
--MS2MassDeviation.standardMassDeviation=10.0 ppm
--NoiseThresholdSettings.absoluteThreshold=0
--NoiseThresholdSettings.basePeak=NOT_PRECURSOR
--NoiseThresholdSettings.intensityThreshold=0.005
--NoiseThresholdSettings.maximalNumberOfPeaks=60
--NumberOfCandidates=10
--NumberOfCandidatesPerIon=1
use this parameter if you want to force to report at
least
numberOfResultsToKeepPerIonization results per
ionization.
if le 0, this parameter will have no effect and just
the top
numberOfResultsToKeep results will be reported.
--NumberOfStructureCandidates=10000
--PossibleAdductSwitches=[M+Na]+:[M+H]+,[M+K]+:[M+H]+,[M+Cl]-:[M-H]-
An adduct switch is a switch of the ionization mode
within a spectrum, e.g. an ion replaces an
sodium adduct
with a protonation during fragmentation. Such adduct
switches heavily increase the
complexity of the
analysis, but for certain adducts they might happen
regularly. Adduct switches are written
in the
form {@literal a -> b, a -> c, d -> c} where a, b,
c, and d are adducts and {@literal a -> b}
denotes an
allowed switch from
a to b within the MS/MS spectrum.
--PrintCitations=True
--RecomputeResults=False
--StructurePredictors=CSI_FINGERID
--StructureSearchDB=BIO
--Timeout.secondsPerInstance=0
This configurations define a timeout for the tree
computation. As the underlying problem is
NP-hard, it might take
forever to compute trees for very challenging (e.g.
large mass) compounds. Setting an time
constraint allow the program
to continue with other instances and just skip the
challenging ones.
Note that, due to multithreading, this time
constraints are not absolutely accurate.
Set the maximum number of seconds for computing a
single compound. Set to 0 to disable the time
constraint.
--Timeout.secondsPerTree=0
Set the maximum number of seconds for a single
molecular formula check. Set to 0 to disable the
time constraint
--UseHeuristic.mzToUseHeuristic=300
Set minimum m/z to enable heuristic preprocessing.
The heuristic will be used to initially
rank the formula candidates. The Top
(NumberOfCandidates) candidates will then be
computed exactly by solving the ILP.
--UseHeuristic.mzToUseHeuristicOnly=650
Set minimum m/z to only use heuristic tree
computation. No exact tree computation (ILP) will
be performed for this compounds.
-V, --version Print version information and exit.
--ZodiacClusterCompounds=false
cluster compounds before running ZODIAC
--ZodiacEdgeFilterThresholds.minLocalCandidates=1
Minimum number of candidates per compound which are
forced to have at least
[minLocalConnections] connections to other compounds.
E.g. 2 candidates per compound must have at least 10
connections to other compounds
--ZodiacEdgeFilterThresholds.minLocalConnections=10
Minimum number of connections per candidate which
are forced for at least
[minLocalCandidates] candidates to other compounds.
E.g. 2 candidates per compound must have at least 10
connections to other compounds
--ZodiacEdgeFilterThresholds.thresholdFilter=0.95
Defines the proportion of edges of the complete
network which will be ignored.
--ZodiacEpochs.burnInPeriod=2000
Number of epochs considered as 'burn-in period'.
Samples from the beginning of a Markov chain do not
accurately represent the desired
distribution of candidates and are not used to
estimate the ZODIAC score.
--ZodiacEpochs.iterations=20000
Number of epochs to run the Gibbs sampling. When
multiple Markov chains are computed, all
chains' iterations sum up to this value.
--ZodiacEpochs.numberOfMarkovChains=10
Number of separate Gibbs sampling runs.
--ZodiacLibraryScoring.lambda=1000
Lambda used in the scoring function of spectral
library hits. The higher this value the higher
are librar hits weighted in ZODIAC scoring.
--ZodiacLibraryScoring.minCosine=0.5
Spectral library hits must have at least this cosine
or higher to be considered in scoring.
Value must be in [0,1].
--ZodiacNumberOfConsideredCandidatesAt300Mz=10
Maximum number of candidate molecular formulas
(fragmentation trees computed by SIRIUS)
per compound which are considered by ZODIAC.
This is the threshold used for all compounds with mz
below 300 m/z and is used to interpolate the
number of candidates for larger compounds.
If lower than 0, all available candidates are
considered.
--ZodiacNumberOfConsideredCandidatesAt800Mz=50
Maximum number of candidate molecular formulas
(fragmentation trees computed by SIRIUS)
per compound which are considered by ZODIAC.
This is the threshold used for all compounds with mz
above 800 m/z and is used to interpolate the
number of candidates for smaller compounds.
If lower than 0, all available candidates are
considered.
--ZodiacRatioOfConsideredCandidatesPerIonization=0.2
Ratio of candidate molecular formulas (fragmentation
trees computed by SIRIUS) per
compound which are forced for each ionization to be
considered by ZODIAC.
This depends on the number of candidates ZODIAC
considers. E.g. if 50 candidates are
considered and a ratio of 0.2 is set, at least 10
candidates per ionization will be
considered, which might increase the number of
candidates above 50.
--ZodiacRunInTwoSteps=true
As default ZODIAC runs a 2-step approach. First
running 'good quality compounds' only, and
afterwards including the remaining.
Commands:
lcms-align, A <PREPROCESSING> Align and merge compounds of
multiple LCMS Runs. Use this tool if you
want to import from mzML/mzXml
fingerprint <COMPOUND_TOOL> Predict molecular fingerprint
from MS/MS and fragmentation trees for each
compound Individually using CSI:FingerID
fingerprint prediction.
structure, search-structure-db <COMPOUND_TOOL> Search in molecular structure
db for each compound Individually using CSI:
FingerID structure database search.
zodiac, rerank-formulas <DATASET_TOOL> Identify Molecular formulas of
all compounds in a dataset together using
ZODIAC.
canopus, compound-classes <COMPOUND_TOOL> Predict compound categories
for each compound individually based on its
predicted molecular fingerprint (CSI:
FingerID) using CANOPUS.
passatutto <COMPOUND_TOOL> Compute a decoy spectra based
on the fragmentation trees of the given
input spectra. If no molecular formula is
provided in the input, the top scoring
computed formula is used.
formula, tree, sirius <COMPOUND_TOOL> Identify molecular formula
for each compound individually using
fragmentation trees and isotope patterns.
project-space, PS <STANDALONE> Modify a given project Space:
Read project(s) with --input, apply
modification and write the result via
--output. If either --input or --output is
given, the modifications will be made
in-place.
custom-db, DB
<STANDALONE> Generate a custom searchable
structure database. Import multiple files
with compounds as SMILES or InChi into this
DB.
similarity <STANDALONE> Computes the similarity between
all compounds in the dataset and outputs a
matrix of similarities.
decomp <STANDALONE> Small tool to decompose masses
with given deviation, ionization, chemical
alphabet and chemical filter.
mgf-export, MGF <STANDALONE> Exports the spectra of a given
input as mgf.
ftree-export <STANDALONE> Exports the fragmentation trees
of a project into various formats
prediction-export, EPR <STANDALONE> Exports predictions from CSI:
FingerID and CANOPUS.
fingerprinter, FP Compute SIRIUS compatible fingerprints from
PubChem standardized SMILES in tsv format.
gui, GUI Starts the graphical user interface of SIRIUS
asService, rest, REST EXPERIMENTAL/UNSTABLE: Starts SIRIUS as a
background (REST) service that can be
requested via a REST-API
login <STANDALONE> Allows a user to login for
SIRIUS Webservices (e.g. CSI:FingerID or
CANOPUS) and securely store a personal
access token.
settings <STANDALONE> Configure persistent (technical)
settings of SIRIUS (e.g. ProxySettings or
ILP Solver).
install-autocompletion <INSTALL> generates and installs an
Autocompletion-Script with all subcommands.
Default installation is for the current user
write-summaries, W <STANDALONE, POSTPROCESSING> Write Summary
files from a given project-space into the
given project-space or a custom location.
"C:\Program Files\sirius\sirius" formula --help
情報: Running with following arguments: [formula, --help]
Usage: sirius formula [-hV] [--no-isotope-filter] [--no-isotope-score]
[--no-recalibration] [-c=<numberOfCandidates>]
[--candidates-per-ion=<numberOfCandidatesPerIon>]
[--compound-timeout=<instanceTimeout>] [-d=<dbName>[,
<dbName>...]] [-e=<detectableElements>]
[-E=<enforcedElements>] [-f=<candidateFormulas>]
[--heuristic=<mzToUseHeuristic>]
[--heuristic-only=<mzToUseHeuristicOnly>]
[-i=<ionsConsidered>] [-I=<ionsEnforced>] [-p=<profile>]
[--ppm-max=<ppmMax>] [--ppm-max-ms2=<ppmMaxMs2>]
[--solver=<solver>] [--tree-timeout=<treeTimeout>] []
[COMMAND]
<COMPOUND_TOOL> Identify molecular formula for each compound individually using
fragmentation trees and isotope patterns.
--solver, --ilp-solver=<solver>
Set ILP solver to be used for fragmentation
computation. Valid values: 'CLP' (included),
'CPLEX', 'GUROBI'.
For GUROBI and CPLEX environment variables need to
be configure (see Manual).
--no-recalibration Disable Recalibration of input Spectra
--no-isotope-filter Disable molecular formula filter. When filtering is
enabled, molecular formulas are excluded if their
theoretical isotope pattern does not match the
theoretical one, even if their MS/MS pattern has
high score.
--no-isotope-score Disable isotope pattern score.
-h, --help Show this help message and exit.
-V, --version Print version information and exit.
-d, --db, --database=<dbName>[,<dbName>...]
Search formulas in the Union of the given
databases. If no database is given all possible
molecular formulas will be respected (no database
is used).
Example: possible DBs: 'ALL,ALL_BUT_INSILICO,BIO,
PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,
MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,
NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,
PUBCHEMANNOTATIONDRUG,
PUBCHEMANNOTATIONSAFETYANDTOXIC,
PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,
YMDBMINE'
Default: none
--ppm-max=<ppmMax> Maximum allowed mass deviation in ppm for
decomposing masses.
Default: 10.0 ppm
--ppm-max-ms2=<ppmMaxMs2>
Maximum allowed mass deviation in ppm for
decomposing masses in MS2. If not specified, the
same value as for the MS1 is used.
Default: 10.0 ppm
--tree-timeout=<treeTimeout>
Time out in seconds per fragmentation tree
computations. 0 for an infinite amount of time.
Default: 0
--compound-timeout=<instanceTimeout>
Maximal computation time in seconds for a single
compound. 0 for an infinite amount of time.
Default: 0
-p, --profile=<profile> Name of the configuration profile.
Predefined profiles are: `default`, 'qtof',
'orbitrap', 'fticr'.
Default: default
-i, --ions-considered=<ionsConsidered>
the iontype/adduct of the MS/MS data. Example: [M+H]
+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also
provide a comma separated list of adducts.
Default: [M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]
+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-
-I, --ions-enforced=<ionsEnforced>
the iontype/adduct of the MS/MS data. Example: [M+H]
+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also
provide a comma separated list of adducts.
Default: ,
--heuristic-only=<mzToUseHeuristicOnly>
Use only heuristic tree computation compounds >=
the specified m/z.
Default: 650
-e, --elements-considered=<detectableElements>
Set the allowed elements for rare element detection.
Example: `SBrClBSe` to allow the elements S,Br,Cl,B
and Se.
Default: S,Br,Cl,B,Se
-c, --candidates=<numberOfCandidates>
Number of formula candidates in the output.
Default: 10
-E, --elements-enforced=<enforcedElements>
Enforce elements for molecular formula
determination.
Example: CHNOPSCl to allow the elements C, H, N, O,
P, S and Cl. Add numbers in brackets to restrict
the minimal and maximal allowed occurrence of
these elements: CHNOP[5]S[8]Cl[1-2]. When one
number is given then it is interpreted as upper
bound.
Default: C,H,N,O,P
-f, --formulas=<candidateFormulas>
Specify a list of candidate formulas the method
should use. Omit this option if you want to
consider all possible molecular formulas
Default: null
--candidates-per-ion=<numberOfCandidatesPerIon>
Minimum number of candidates in the output for each
ionization. Set to force output of results for
each possible ionization, even if not part of
highest ranked results.
Default: 1
--heuristic=<mzToUseHeuristic>
Enable heuristic preprocessing for compounds >= the
specified m/z.
Default: 300
Commands:
passatutto <COMPOUND_TOOL> Compute a decoy spectra based on the
fragmentation trees of the given input spectra. If
no molecular formula is provided in the input, the
top scoring computed formula is used.
zodiac, rerank-formulas <DATASET_TOOL> Identify Molecular formulas of all
compounds in a dataset together using ZODIAC.
fingerprint <COMPOUND_TOOL> Predict molecular fingerprint from
MS/MS and fragmentation trees for each compound
Individually using CSI:FingerID fingerprint
prediction.
write-summaries, W <STANDALONE, POSTPROCESSING> Write Summary files
from a given project-space into the given
project-space or a custom location.
