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OpenMS
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De novo metabolite identification.
CSI:FingerID (Compound Structure Identification: FingerID) is a method for searching a tandem mass spectrum of a small molecule (metabolite) in a database of molecular structures.
To use this feature, the Sirius command line tool as well as a java installation is needed.
Sirius can be found on https://bio.informatik.uni-jena.de/software/sirius/
Please use Sirius Version 4.0.1
If you want to use the software with the Gurobi solver or CPLEX instead of GLPK, please follow the instructions in the sirius manual.
Internal procedure in SiriusAdapter
The command line parameters of this tool are:
SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry
Full documentation: http://www.openms.de/doxygen/release/3.1.0/html/TOPP_SiriusAdapter.html
Version: 3.1.0 Oct 18 2023, 10:27:18, Revision: 17a07f8
To cite OpenMS:
+ Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for
mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.
To cite SiriusAdapter:
+ Kai Duehrkop and Sebastian Boecker. Fragmentation trees reloaded. J Cheminform; 2016. doi:10.1186/s13321-0
16-0116-8.
+ Kai Duehrkop, Huibin Shen, Marvin Meusel, Juho Rousu, and Sebastian Boecker. Searching molecular structure
databases with tandem mass spectra using CSI:FingerID. Proceedings of the National Academy of Sciences;
2015. doi:10.1073/pnas.1509788112.
Usage:
SiriusAdapter <options>
Options (mandatory options marked with '*'):
-sirius_executable <executable> The Sirius executable. Provide a full or relative path
, or make sure it can be found in your PATH environmen
t.
-in <file>* MzML Input file (valid formats: 'mzML')
-in_featureinfo <file> FeatureXML input with feature and adduct information
(valid formats: 'featureXML')
-out_sirius <file> MzTab output file for SIRIUS results (valid formats:
'mzTab')
-out_fingerid <file> MzTab output file for CSI:FingerID, if this parameter
is given, SIRIUS will search for a molecular structure
using CSI:FingerID after determining the sum formula
(valid formats: 'mzTab')
-out_ms <file> Internal SIRIUS .ms format after OpenMS preprocessing
(valid formats: 'ms')
-out_annotated_spectra <file> Export spectra with fragment annotations from SIRIUS
(valid formats: 'mzML')
-out_project_space <directory> Output directory for SIRIUS project space
-sirius_user_email <string> E-mail for your SIRIUS account.
-sirius_user_password <string> Password for your SIRIUS account.
preprocessing:
-preprocessing:filter_by_num_masstraces <number> Number of mass traces each feature has to have to be
included. To use this parameter, setting the feature_o
nly flag is necessary (default: '1') (min: '1')
-preprocessing:precursor_mz_tolerance <value> Tolerance window for precursor selection (Feature sele
ction in regard to the precursor) (default: '10.0')
-preprocessing:precursor_mz_tolerance_unit <choice> Unit of the precursor_mz_tolerance (default: 'ppm')
(valid: 'Da', 'ppm')
-preprocessing:precursor_rt_tolerance <value> Tolerance window (left and right) for precursor select
ion [seconds] (default: '5.0')
-preprocessing:isotope_pattern_iterations <number> Number of iterations that should be performed to extra
ct the C13 isotope pattern. If no peak is found (C13
distance) the function will abort. Be careful with
noisy data - since this can lead to wrong isotope patt
erns (default: '3')
-preprocessing:feature_only Uses the feature information from in_featureinfo to
reduce the search space to MS2 associated with a featu
re
-preprocessing:no_masstrace_info_isotope_pattern Use this flag if the masstrace information from a feat
ure should be discarded and the isotope_pattern_iterat
ions should be used instead
project:
-project:maxmz <number> Just consider compounds with a precursor mz lower or
equal
this maximum mz. All other compounds in the input file
are ignored. (default: '-1')
-project:loglevel <text> Set logging level of the Jobs SIRIUS will execute.
Valid values: SEVERE, WARNING, INFO, FINER, ALL
Default: WARNING
-project:ignore_formula Ignore given molecular formula in internal .ms format,
while processing.
-project:q Suppress shell output
sirius:
-sirius:ppm_max <value> Maximum allowed mass deviation in ppm for decomposing
masses [ppm]. (default: '10.0')
-sirius:ppm_max_ms2 <value> Maximum allowed mass deviation in ppm for decomposing
masses in MS2 [ppm].If not specified, the same value
as for the MS1 is used. (default: '10.0')
-sirius:tree_timeout <number> Time out in seconds per fragmentation tree computation
s. 0 for an infinite amount of time (default: '100')
(min: '0')
-sirius:compound_timeout <number> Maximal computation time in seconds for a single compo
und. 0 for an infinite amount of time. (default: '100'
) (min: '0')
-sirius:no_recalibration Disable recalibration of input spectra
-sirius:profile <choice> Name of the configuration profile (default: 'default')
(valid: 'default', 'qtof', 'orbitrap', 'fticr')
-sirius:formulas <text> Specify the neutral molecular formula of the measured
compound to compute its tree or a list of candidate
formulas the method should discriminate. Omit this
option if you want to consider all possible molecular
formulas
-sirius:ions_enforced <text> 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.
-sirius:candidates <number> The number of formula candidates in the SIRIUS output
(default: '10') (min: '0')
-sirius:candidates_per_ion <number> 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 ranke
d results. (default: '1')
-sirius:elements_considered <text> Set the allowed elements for rare element detection.
Write SBrClBSe to allow the elements S,Br,Cl,B and
Se. (default: 'SBrClBSe')
-sirius:elements_enforced <text> Enforce elements for molecular formula determination.
Write CHNOPSCl to allow the elements C, H, N, O, P, S
and Cl. Add numbers in brackets to restrict the minima
l 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: 'CHNOP')
-sirius:no_isotope_score Disable isotope pattern score.
-sirius:no_isotope_filter Disable molecular formula filter. When filtering is
enabled, molecular formulas are excluded if their theo
retical isotope pattern does not match the theoretical
one, even if their MS/MS pattern has high score.
-sirius:ions_considered <text> 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]-')
-sirius:db <text> Search formulas in the Union of the given databases
db-name1,db-name2,db-name3. If no database is given
all possible molecular formulas will be respected (no
database is used). Example: possible DBs: ALL,BIO,PUBC
HEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,
METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIO
NAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEM
ANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMIN
E,ECOCYCMINE,YMDBMINE (default: 'none')
-sirius:solver <text> For GUROBI and CPLEX environment variables need to be
configured.
(see SIRIUS manual: https://boecker-lab.github.io/docs
.sirius.github.io/install/). (default: 'CLP')
fingerid:
-fingerid:db <text> Search structures in the Union of the given databases
db-name1,db-name2,db-name3. If no database is given
all possible molecular formulas will be respected (no
database is used). Example: possible DBs: ALL,BIO,PUBC
HEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,
METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIO
NAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEM
ANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMIN
E,ECOCYCMINE,YMDBMINE
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the
TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
INI file documentation of this tool:
1.9.1