Sirius formula identification#

COMPOUND TOOL

Functionality#

Identify molecular formula for each compound individually using fragmentation trees and isotope patterns.

Options#

Option

Description

--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 a high score.

--no-isotope-score

Disable isotope pattern score.

--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 configured (see Manual).

-h, --help

Show this help message and exit.

-V, --version

Print version information and exit.

--candidates-per-ion=<numberOfCandidatesPerIon>

Minimum number of candidates in the output for each ionization. Set to force the output of results for each possible ionization, even if not part of the highest-ranked results. Default: 1

--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>

Timeout 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

-c, --candidates=<numberOfCandidates>

Number of formula candidates in the output. Default: 10

-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

-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 an 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

-i, --ions-considered=<ionsConsidered>

The ion type/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 ion type/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: none

--heuristic=<mzToUseHeuristic>

Enable heuristic preprocessing for compounds >= the specified m/z. Default: 300

--heuristic-only=<mzToUseHeuristicOnly>

Use only heuristic tree computation for compounds >= the specified m/z. Default: 650

-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

-p, --profile=<profile>

Name of the configuration profile. Predefined profiles are: default, ‘qtof’, ‘orbitrap’, ‘fticr’. Default: default

Follow-up commands#

  • passatutto - 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 - Identify molecular formulas of all compounds in a dataset together using ZODIAC.

  • fingerprint - Predict molecular fingerprint from MS/MS and fragmentation trees for each compound individually using CSI:FingerID fingerprint prediction.

  • write-summaries, W - Write summary files from a given project-space into the given project-space or a custom location.