Predict formula and structure of chromatographic peaks from an XcmsExperiment object Sirius through the RuSirius package.
Source:vignettes/Chromatographic_peak_annotation_public_dataset.Rmd
Chromatographic_peak_annotation_public_dataset.Rmd
library(Spectra)
library(MsExperiment)
library(xcms)
library(RSirius)
library(MetaboAnnotation)
library(RuSirius)
library(dplyr)
library(MsDataHub)Introduction
Note: this vignette is pre-computed. See the session info for information on packages used and the date the vignette was rendered. The vignette requires a running Sirius instance and a Sirius account for structure database searches. To reproduce this analysis, you will need to log in to your own Sirius account.
This vignette demonstrates a basic workflow for importing detected
chromatographic peaks from an XcmsExperiment
object into Sirius. It then runs Sirius’s main tools: formula
identification, structure database search, compound class prediction,
spectral library matching, de novo structure prediction, and
finally retrieves the results.
This is a foundational example and does not cover all the possible
parameters for each Sirius tool. For detailed parameter information,
consult the run() function documentation. More information
can be found in the Sirius
documentation online.
While this vignette focuses on chromatographic peaks detected with xcms, a similar workflow applies to features (grouped chromatographic peaks). The vignette for features is pending the availability of public data, but the steps for data preparation differ only slightly and can be adapted without issue.
IMPORTANT: This is a work in progress. Feedback is highly valued, especially regarding enhancements or additions that could simplify your workflow. Your input as a user is essential.
Preprocessing
Here, we apply pre-optimized parameters for processing the example dataset.
dda_file <- MsDataHub::PestMix1_DDA.mzML()
dda_data <- readMsExperiment(dda_file)
spectra(dda_data) <- setBackend(spectra(dda_data), MsBackendMemory())
dda_data <- filterRt(dda_data, rt = c(230, 610))
dda_data |>
spectra() |>
msLevel() |>
table()
#>
#> 1 2
#> 1389 2214
prec_int <- estimatePrecursorIntensity(spectra(dda_data))
cwp <- CentWaveParam(snthresh = 5, noise = 100, ppm = 10,
peakwidth = c(3, 30))
dda_data <- findChromPeaks(dda_data, param = cwp, msLevel = 1L)MS1 and MS2 Extraction
MS2 and MS1 spectra corresponding to the identified chromatographic peaks are extracted. Each feature imported in Sirius can only have one MS1 spectrum. However MS2 can also be loaded by itself wiht no MS1 if wanted.
# Extract MS1 and MS2 spectra linked to chromatographic peaks
ms2 <- chromPeakSpectra(dda_data,
expandMz = 0.01, expandRt = 3,
msLevel = 2L)
low_int <- function(x, ...) x > max(x, na.rm = TRUE) * 0.05
ms2 <- filterIntensity(ms2, intensity = low_int)
ms2 <- ms2[lengths(ms2) > 1]
ms1 <- chromPeakSpectra(dda_data,
expandMz = 0.01, expandRt = 3,
msLevel = 1L, method = "closest_rt")
ms1 <- applyProcessing(ms1)
ms2 <- applyProcessing(ms2)
ms1_ms2 <- concatenateSpectra(ms1, ms2)Open Sirius and project set up
The Sirius application is initialized via the API, requiring only a
project ID. If the project exists, it is opened; otherwise, a new
project is created. The srs object acts as the connection
to Sirius and holds project details. Properly shut down the connection
with shutdown(srs) after completing your work.
This srs variable is needed for any task that
necessitate to communicate with the application. You can learn more
about this object class by running ?Sirius in the console.
Parameter port used below allows to configure the
Sirius application to use a particular port, but generally the
function can be used without specifying a port.
# Initialize Sirius connection
srs <- Sirius(projectId = "test_lcmsms", port = 9999)
#> Found SIRIUS in PATH! Using this information to start the application.
#> SIRIUS was started without specifying --port (-p), trying to find the sirius.port file.
srs
#> Sirius object
#> Valid connection to Sirius: TRUE
#> Logged In: TRUE
#> Sirius version: 6.3.3
#> Sirius update available: FALSE
#> Project ID: test_lcmsms
#> Number of features in the project: 0
#> No job was run/is running on this project.If the user wants to open and perform computations on a different project they can use the utility function below:
srs <- openProject(srs, projectId = "test_lcmsms2", path = getwd())
srs
#> Sirius object
#> Valid connection to Sirius: TRUE
#> Logged In: TRUE
#> Sirius version: 6.3.3
#> Sirius update available: FALSE
#> Project ID: test_lcmsms2
#> Number of features in the project: 0
#> No job was run/is running on this project.You can find all the utility functions of this package by running
?utils in the console.
NOTE if you have any idea of utility functions that could be implemented do not hesitate to ask.
Data import
Preprocessed xcms data is imported into Sirius, and a
summary data.frame is returned with feature information.
This information can also be retrieved using the utility function
featuresInfo().
## load back our original project
srs <- openProject(srs, "test_lcmsms")
## Import data into Sirius
srs <- import(sirius = srs,
spectra = ms1_ms2,
ms_column_name = "chrom_peak_id",
deleteExistingFeatures = TRUE)
## See information about the features
featuresInfo(srs) |> head()
#> alignedFeatureId
#> [1,] "819205328622094770"
#> [2,] "819205328718563763"
#> [3,] "819205328735340980"
#> [4,] "819205328781478325"
#> [5,] "819205328798255542"
#> [6,] "819205328810838455"
#> compoundId
#> [1,] "819205328445933888"
#> [2,] "819205328445933889"
#> [3,] "819205328445933890"
#> [4,] "819205328445933891"
#> [5,] "819205328445933892"
#> [6,] "819205328445933893"
#> externalFeatureId
#> [1,] "CP001"
#> [2,] "CP002"
#> [3,] "CP003"
#> [4,] "CP004"
#> [5,] "CP005"
#> [6,] "CP006"
#> ionMass charge
#> [1,] 0 1
#> [2,] 0 1
#> [3,] 220.0975 1
#> [4,] 219.0932 1
#> [5,] 153.0656 1
#> [6,] 235.1442 1
#> detectedAdducts hasMs1
#> [1,] list,1 TRUE
#> [2,] list,1 TRUE
#> [3,] list,1 TRUE
#> [4,] list,1 TRUE
#> [5,] list,1 TRUE
#> [6,] list,1 TRUE
#> hasMsMs computing
#> [1,] FALSE FALSE
#> [2,] FALSE FALSE
#> [3,] TRUE FALSE
#> [4,] TRUE FALSE
#> [5,] TRUE FALSE
#> [6,] TRUE FALSENotes:
- It could also be discussed that this
data.framecould be stored direction into thesrsobject - When running
import()i automatically create a mapping data.frame between the xcms feature ID and the Sirius feature ID. It is stored in thesrsobject, thefeatureMapslot. This can be used in the future so the user never need to interact with the Sirius IDs.
Below is an example of how to extract features ID, the utility
function featuresId() quickly extract all available ID
either sirius or xcms.
fts_id <- featuresId(srs, type = "sirius")Searchable database
!!! Note: The database code does not work at the moment, please load them through the GUI until it’s fixed. !!!
Whether it is for structure prediction or spectral library matching,
users can upload their custom databases into Sirius. In this vignette,
we demonstrate how to test spectral library matching by creating and
loading a custom database into Sirius. This process can also be
completed easily via the Sirius graphical user interface (GUI). If you
prefer an interactive approach, you can use the
openGUI(srs) command to open the Sirius app and manage your
database directly.
In this example, we download the MassBank library from GNPS, which
needs to be loaded into Sirius to generate a .sirius.db
file. Below we will download in our current directory but you can
precise where you want to save it using location =
parameter.
## Download the MassBank EU library
download.file("https://external.gnps2.org/gnpslibrary/MASSBANKEU.mgf",
destfile = "MASSBANKEU.mgf")
createDb(srs, databaseId = "massbankeuCustom", files = "MASSBANKEU.mgf")NOTE: THis takes quite a while, will change to a smaller database later. Once the database is created and loaded, you can verify its successful import by running the following command:
listDbs(srs)Find more on how to handle databases in Sirius by typing
?siriusDBs in the console.
Submit job to Sirius - For structure DB search
Annotation and prediction begin after data import. The
run() function accepts parameters for each Sirius tool,
such as formula identification, structure database search, and compound
class prediction. Parameters can also specify adducts or custom
databases. Detailed documentation for these parameters is available in
the run() function’s help file.
The wait parameter ensures the function waits for job
completion before proceeding. If set to FALSE, the job ID
is returned, and the user must check the status using
jobInfo().
## Start computation
job_id <- run(srs,
fallbackAdducts = c("[M + H]+", "[M + Na]+", "[M + K]+"),
formulaIdParams = formulaIdParam(numberOfCandidates = 5,
instrument = "QTOF",
numberOfCandidatesPerIonization = 2,
massAccuracyMS2ppm = 10,
filterByIsotopePattern = FALSE,
isotopeMs2Settings = c("SCORE"),
performDeNovoBelowMz = 600,
minPeaksToInjectSpecLibMatch = 3),
predictParams = predictParam(),
structureDbSearchParams = structureDbSearchParam(
structureSearchDbs = c("BIO")
),
recompute = TRUE,
wait = TRUE
)
srs
#> Sirius object
#> Valid connection to Sirius: TRUE
#> Logged In: TRUE
#> Sirius version: 6.3.3
#> Sirius update available: FALSE
#> Project ID: test_lcmsms
#> Number of features in the project: 114
#> Job ids available: 1
#> State of latest job: DONE
## Get more info for the job
jobInfo(srs, job_id) |> cat()
#> Job ID: 1
#>
#> Command:
#> --IsotopeSettings.filter=false
#> --InjectSpectralLibraryMatchFormulas.minPeakMatchesToInject=3
#> --FormulaSettings.enforced=HCNOP
#> --InjectSpectralLibraryMatchFormulas.injectFormulas=true
#> --TagStructuresByElGordo=true
#> --AdductSettings.detectable=[M+H3N+H]+,[M-H4O2+H]+,[M-H2O-H]-,[M-H3N-H]-,[M+Cl]-,[2M+K]+,[M+K]+,[2M+Cl]-,[M+C2H4O2-H]-,[M+H]+,[2M+H]+,[M-CH3-H]-,[M-H]-,[M+Na]+,[M-H2O+H]+
#> --RecomputeResults=true
#> --UseHeuristic.useHeuristicAboveMz=300
#> --IsotopeMs2Settings=SCORE
#> --MS2MassDeviation.allowedMassDeviation=10.0ppm
#> --FormulaSearchSettings.applyFormulaConstraintsToDatabaseCandidates=false
#> --EnforceElGordoFormula=true
#> --NumberOfCandidatesPerIonization=2
#> --AdductSettings.fallback=[M+H]+,[M+Na]+,[M+K]+
#> --FormulaSearchSettings.performBottomUpAboveMz=0.0
#> --FormulaSettings.fallback=S
#> --FormulaSearchSettings.applyFormulaConstraintsToBottomUp=false
#> --UseHeuristic.useOnlyHeuristicAboveMz=650
#> --ExpansiveSearchConfidenceMode.confidenceScoreSimilarityMode=APPROXIMATE
#> --InjectSpectralLibraryMatchFormulas.minScoreToInject=0.7
#> --FormulaSearchDB=
#> --FormulaResultThreshold=true
#> --InjectSpectralLibraryMatchFormulas.alwaysPredict=false
#> --FormulaSettings.detectable=B,S,Cl,Se,Br
#> --NumberOfCandidates=5
#> formulas
#> fingerprints
#> classes
#> structures
#>
#> Progress:
#> State: DONE
#> Current Progress: 58240
#> Max Progress: 58240
#>
#> Affected Compound IDs:
#> 819205328450128305, 819205328450128304, 819205328450128303, 819205328450128302, 819205328450128301, 819205328450128300, 819205328450128299, 819205328450128298, 819205328450128297, 819205328450128296, 819205328450128295, 819205328450128294, 819205328450128293, 819205328450128292, 819205328450128291, 819205328450128290, 819205328450128289, 819205328450128288, 819205328445933983, 819205328445933982, 819205328445933981, 819205328445933980, 819205328445933979, 819205328445933978, 819205328445933977, 819205328445933976, 819205328445933975, 819205328445933974, 819205328445933973, 819205328445933972, 819205328445933971, 819205328445933970, 819205328445933969, 819205328445933968, 819205328445933967, 819205328445933966, 819205328445933965, 819205328445933964, 819205328445933963, 819205328445933962, 819205328445933961, 819205328445933960, 819205328445933959, 819205328445933958, 819205328445933957, 819205328445933956, 819205328445933955, 819205328445933954, 819205328445933953, 819205328445933952, 819205328445933951, 819205328445933950, 819205328445933949, 819205328445933948, 819205328445933947, 819205328445933946, 819205328445933945, 819205328445933944, 819205328445933943, 819205328445933942, 819205328445933941, 819205328445933940, 819205328445933939, 819205328445933938, 819205328445933937, 819205328445933936, 819205328445933935, 819205328445933934, 819205328445933933, 819205328445933932, 819205328445933931, 819205328445933930, 819205328445933929, 819205328445933928, 819205328445933927, 819205328445933926, 819205328445933925, 819205328445933924, 819205328445933923, 819205328445933922, 819205328445933921, 819205328445933920, 819205328445933919, 819205328445933918, 819205328445933917, 819205328445933916, 819205328445933915, 819205328445933914, 819205328445933913, 819205328445933912, 819205328445933911, 819205328445933910, 819205328445933909, 819205328445933908, 819205328445933907, 819205328445933906, 819205328445933905, 819205328445933904, 819205328445933903, 819205328445933902, 819205328445933901, 819205328445933900, 819205328445933899, 819205328445933898, 819205328445933897, 819205328445933896, 819205328445933895, 819205328445933894, 819205328445933893, 819205328445933892, 819205328445933891, 819205328445933890, 819205328445933889, 819205328445933888
#>
#> Affected Aligned Feature IDs:
#> 819205329515481635
#> 819205329511287330
#> 819205329511287329
#> 819205329502898720
#> 819205329502898719
#> 819205329502898718
#> 819205329502898717
#> 819205329498704412
#> 819205329498704411
#> 819205329498704410
#> 819205329498704409
#> 819205329494510104
#> 819205329494510103
#> 819205329490315798
#> 819205329486121493
#> 819205329486121492
#> 819205329481927187
#> 819205329481927186
#> 819205329477732881
#> 819205329473538576
#> 819205329469344271
#> 819205329465149966
#> 819205329465149965
#> 819205329456761356
#> 819205329456761355
#> 819205329452567050
#> 819205329448372745
#> 819205329448372744
#> 819205329444178439
#> 819205329444178438
#> 819205329439984133
#> 819205329439984132
#> 819205329435789827
#> 819205329435789826
#> 819205329431595521
#> 819205329427401216
#> 819205329427401215
#> 819205329423206910
#> 819205329423206909
#> 819205329419012604
#> 819205329414818299
#> 819205329414818298
#> 819205329410623993
#> 819205329406429688
#> 819205329402235383
#> 819205329393846774
#> 819205329393846773
#> 819205329389652468
#> 819205329385458163
#> 819205329381263858
#> 819205329372875249
#> 819205329372875248
#> 819205329368680943
#> 819205329326737902
#> 819205329322543597
#> 819205329318349292
#> 819205329301572075
#> 819205329297377770
#> 819205329293183465
#> 819205329259629032
#> 819205329255434727
#> 819205329251240422
#> 819205329247046117
#> 819205329242851812
#> 819205329242851811
#> 819205329238657506
#> 819205329234463201
#> 819205329230268896
#> 819205329230268895
#> 819205329226074590
#> 819205329213491677
#> 819205329209297372
#> 819205329200908763
#> 819205329179937242
#> 819205329179937241
#> 819205329175742936
#> 819205329175742935
#> 819205329171548630
#> 819205329167354325
#> 819205329163160020
#> 819205329117022675
#> 819205329112828370
#> 819205329108634065
#> 819205329108634064
#> 819205329096051151
#> 819205329096051150
#> 819205329096051149
#> 819205329091856844
#> 819205329087662539
#> 819205329079273930
#> 819205329075079625
#> 819205329066691016
#> 819205329058302407
#> 819205329054108102
#> 819205329041525189
#> 819205329028942276
#> 819205329012165059
#> 819205328995387842
#> 819205328982804929
#> 819205328970222016
#> 819205328932473279
#> 819205328919890366
#> 819205328903113149
#> 819205328886335932
#> 819205328869558715
#> 819205328861170106
#> 819205328844392889
#> 819205328831809976
#> 819205328810838455
#> 819205328798255542
#> 819205328781478325
#> 819205328735340980
#> 819205328718563763
#> 819205328622094770Retrieve Results
To obtain a summary of all results, including the top formulas, structures, and compound class predictions, use the following code. This summary table provides a quick overview to evaluate whether the results align with expectations. However, we recommend not relying on this table as-is for detailed analysis. Instead, use the functions described later in this vignette to explore the results in greater depth.
An important aspect of the summary table is the confidence-related columns, which provide insight into the reliability of the predictions.
summarytb <- summary(sirius = srs, result.type = "structure")
head(summarytb)
#> alignedFeatureId
#> 1 819205328622094770
#> 2 819205328718563763
#> 3 819205328735340980
#> 4 819205328781478325
#> 5 819205328798255542
#> 6 819205328810838455
#> compoundId
#> 1 819205328445933888
#> 2 819205328445933889
#> 3 819205328445933890
#> 4 819205328445933891
#> 5 819205328445933892
#> 6 819205328445933893
#> externalFeatureId ionMass
#> 1 CP001 0.0000
#> 2 CP002 0.0000
#> 3 CP003 220.0975
#> 4 CP004 219.0932
#> 5 CP005 153.0656
#> 6 CP006 235.1442
#> charge hasMs1 hasMsMs
#> 1 1 TRUE FALSE
#> 2 1 TRUE FALSE
#> 3 1 TRUE TRUE
#> 4 1 TRUE TRUE
#> 5 1 TRUE TRUE
#> 6 1 TRUE TRUE
#> formulaId
#> 1 819205523682397402
#> 2 819205528308714745
#> 3 819205520754773184
#> 4 819205514274573431
#> 5 819205517835537577
#> 6 819205510843632741
#> molecularFormula
#> 1 C6H12N6O3
#> 2 C10H16O5
#> 3 C10H10FN5
#> 4 C12H14N2S
#> 5 C4H6FNO3
#> 6 C10H19FN2O3
#> adduct rank
#> 1 [M + H]+ 1
#> 2 [M + H]+ 1
#> 3 [M + H]+ 2
#> 4 [M + H]+ 1
#> 5 [M + H3N + H]+ 2
#> 6 [M + H]+ 1
#> siriusScoreNormalized
#> 1 0.08222814
#> 2 0.07231049
#> 3 0.09484521
#> 4 0.94680986
#> 5 0.49999999
#> 6 0.99585317
#> siriusScore isotopeScore
#> 1 0.000000 0.000000
#> 2 0.000000 0.000000
#> 3 6.372408 0.000000
#> 4 48.071033 0.000000
#> 5 27.906019 1.966055
#> 6 27.272863 4.595855
#> treeScore computing
#> 1 0.000000 FALSE
#> 2 0.000000 FALSE
#> 3 6.372408 FALSE
#> 4 48.071033 FALSE
#> 5 25.939964 FALSE
#> 6 22.677008 FALSE
#> inchiKey
#> 1 <NA>
#> 2 <NA>
#> 3 LYCFRYBMIAOVRF
#> 4 YUAUPYJCVKNAEC
#> 5 VNYARQMKDIBKDQ
#> 6 FYBNLUNYTZMQQZ
#> smiles
#> 1 <NA>
#> 2 <NA>
#> 3 CC1=CC(=C(C=C1)NC2=NC=NC(=N2)N)F
#> 4 CC1=CC(=C(C=C1)N=C2N(C=CS2)C)C
#> 5 C(C[N+](=O)[O-])C(=O)CF
#> 6 C1CN(CCC1N(CCCCO)F)C(=O)O
#> structureName
#> 1 <NA>
#> 2 <NA>
#> 3 2-N-(2-fluoro-4-methylphenyl)-1,3,5-triazine-2,4-diamine
#> 4 <NA>
#> 5 1-Fluoro-4-nitrobutane-2-one
#> 6 4-[Fluoro(4-hydroxybutyl)amino]piperidine-1-carboxylic acid
#> xlogP rank.1 csiScore
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 2.0 1 -95.92160
#> 4 3.0 1 -76.43829
#> 5 0.1 1 -172.54632
#> 6 -1.8 1 -278.49182
#> tanimotoSimilarity
#> 1 NA
#> 2 NA
#> 3 0.4936709
#> 4 0.6708861
#> 5 0.1166667
#> 6 0.2803030
#> mcesDistToTopHit type
#> 1 NA <NA>
#> 2 NA <NA>
#> 3 0 NPC
#> 4 0 NPC
#> 5 0 NPC
#> 6 0 NPC
#> level levelIndex
#> 1 <NA> NA
#> 2 <NA> NA
#> 3 PATHWAY 0
#> 4 PATHWAY 0
#> 5 PATHWAY 0
#> 6 PATHWAY 0
#> name
#> 1 <NA>
#> 2 <NA>
#> 3 Alkaloids
#> 4 Alkaloids
#> 5 Fatty acids
#> 6 Alkaloids
#> description id
#> 1 <NA> NA
#> 2 <NA> NA
#> 3 Pathway: Alkaloids 0
#> 4 Pathway: Alkaloids 0
#> 5 Pathway: Fatty acids 3
#> 6 Pathway: Alkaloids 0
#> probability index type.1
#> 1 NA NA <NA>
#> 2 NA NA <NA>
#> 3 0.8597484 0 NPC
#> 4 0.6377908 0 NPC
#> 5 0.3361939 3 NPC
#> 6 0.2922554 0 NPC
#> level.1 levelIndex.1
#> 1 <NA> NA
#> 2 <NA> NA
#> 3 SUPERCLASS 1
#> 4 SUPERCLASS 1
#> 5 SUPERCLASS 1
#> 6 SUPERCLASS 1
#> name.1
#> 1 <NA>
#> 2 <NA>
#> 3 Pseudoalkaloids (transamidation)
#> 4 Tryptophan alkaloids
#> 5 Fatty Acids and Conjugates
#> 6 Pseudoalkaloids (transamidation)
#> description.1
#> 1 <NA>
#> 2 <NA>
#> 3 Superclass: Pseudoalkaloids (transamidation)
#> 4 Superclass: Tryptophan alkaloids
#> 5 Superclass: Fatty Acids and Conjugates
#> 6 Superclass: Pseudoalkaloids (transamidation)
#> id.1 probability.1 index.1
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 59 0.14546104 59
#> 4 72 0.08722231 72
#> 5 24 0.12120167 24
#> 6 59 0.32983977 59
#> type.2 level.2 levelIndex.2
#> 1 <NA> <NA> NA
#> 2 <NA> <NA> NA
#> 3 NPC CLASS 2
#> 4 NPC CLASS 2
#> 5 NPC CLASS 2
#> 6 NPC CLASS 2
#> name.2
#> 1 <NA>
#> 2 <NA>
#> 3 Purine alkaloids
#> 4 Pyridine alkaloids
#> 5 Halogenated fatty acids
#> 6 Purine alkaloids
#> description.2
#> 1 <NA>
#> 2 <NA>
#> 3 Class: Purine alkaloids
#> 4 Class: Pyridine alkaloids
#> 5 Class: Halogenated fatty acids
#> 6 Class: Purine alkaloids
#> id.2 probability.2 index.2
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 597 0.06170827 597
#> 4 602 0.05239901 602
#> 5 376 0.57457018 376
#> 6 597 0.13299610 597
#> confidenceExactMatch
#> 1 <NA>
#> 2 <NA>
#> 3 0.0771017862497153
#> 4 0.456098397132935
#> 5 0.0229246504272595
#> 6 0.00421334090615453
#> confidenceApproxMatch
#> 1 <NA>
#> 2 <NA>
#> 3 0.0771017862497153
#> 4 0.456098397132935
#> 5 0.0229246504272595
#> 6 0.00421334090615453
#> expansiveSearchState
#> 1 <NA>
#> 2 <NA>
#> 3 APPROXIMATE
#> 4 OFF
#> 5 OFF
#> 6 APPROXIMATEFormula identification results:
For detailed results, the results() function can be used with the
result.type parameter set to "formulaId",
"structureDb", "compoundClass", or
"deNovo". Note that all results are linked to a predicted
formula.
The parameters topFormula and topStructure
allow users to specify how many formulas or structures should be
included in the output. The results can be returned either as a list or
a data.frame, based on the return.type parameter.
Note: Suggestions for renaming the results() function or
feedback on this implementation are welcome. We aim to adapt based on
user needs.
results(srs,
return.type = "data.frame",
result.type = "formulaId",
topFormula = 5)
#> formulaId
#> 1 819205523682397402
#> 2 819205523682397403
#> 3 819205523682397404
#> 4 819205523682397405
#> 5 819205523682397406
#> 6 819205528308714745
#> 7 819205528308714746
#> 8 819205528308714747
#> 9 819205528308714748
#> 10 819205528308714749
#> 11 819205520754773183
#> 12 819205520754773184
#> 13 819205520754773185
#> 14 819205520754773186
#> 15 819205520754773187
#> 16 819205514274573431
#> 17 819205514274573432
#> 18 819205514274573433
#> 19 819205514274573434
#> 20 819205514274573435
#> 21 819205517835537576
#> 22 819205517835537577
#> 23 819205517835537578
#> 24 819205517835537579
#> 25 819205517835537580
#> 26 819205510843632741
#> 27 819205510843632742
#> 28 819205510843632743
#> 29 819205510843632744
#> 30 819205510843632745
#> 31 819205526358363380
#> 32 819205526358363381
#> 33 819205526358363382
#> 34 819205526358363383
#> 35 819205526358363384
#> 36 819205507509161048
#> 37 819205507509161049
#> 38 819205507509161050
#> 39 819205516493360272
#> 40 819205516493360273
#> 41 819205516493360274
#> 42 819205516493360275
#> 43 819205516493360276
#> 44 819205504191466564
#> 45 819205504191466565
#> 46 819205504191466566
#> 47 819205504191466567
#> 48 819205504191466568
#> 49 819205543399820581
#> 50 819205543399820582
#> 51 819205543399820583
#> 52 819205543399820584
#> 53 819205543399820585
#> 54 819205525842463972
#> 55 819205525842463973
#> 56 819205525842463974
#> 57 819205525842463975
#> 58 819205525842463976
#> 59 819205524462537952
#> 60 819205524462537953
#> 61 819205524462537954
#> 62 819205524462537955
#> 63 819205512961756275
#> 64 819205512961756276
#> 65 819205512961756277
#> 66 819205522893868246
#> 67 819205522893868247
#> 68 819205522893868248
#> 69 819205522893868249
#> 70 819205506200538186
#> 71 819205506200538187
#> 72 819205506200538188
#> 73 819205506200538189
#> 74 819205506200538190
#> 75 819205490031496201
#> 76 819205490031496202
#> 77 819205490031496203
#> 78 819205517218974873
#> 79 819205517218974874
#> 80 819205517218974875
#> 81 819205517218974876
#> 82 819205517218974877
#> 83 819205518573735089
#> 84 819205518573735090
#> 85 819205518573735091
#> 86 819205518573735092
#> 87 819205518573735093
#> 88 819205464869866386
#> 89 819205464874060691
#> 90 819205464874060692
#> 91 819205464874060693
#> 92 819205464874060694
#> 93 819205517743262880
#> 94 819205517743262881
#> 95 819205517743262882
#> 96 819205517743262883
#> 97 819205517743262884
#> 98 819205480292322241
#> 99 819205480292322242
#> 100 819205480292322243
#> molecularFormula
#> 1 C6H12N6O3
#> 2 C8H15F3O3
#> 3 C8H18O5
#> 4 C9H14N4O
#> 5 C6H18N4O2
#> 6 C10H16O5
#> 7 C6H12N6O3
#> 8 C8H18O5
#> 9 C9H14N4O
#> 10 C8H20NO3
#> 11 C9H14FNO4
#> 12 C10H10FN5
#> 13 C12H13NO3
#> 14 C9H15F2NOSi
#> 15 C5H13F2N5O
#> 16 C12H14N2S
#> 17 C6H13F3N2O3
#> 18 C11H16ClFO
#> 19 C10H16FO2P
#> 20 C12H17F
#> 21 C4H9FN2O3
#> 22 C4H6FNO3
#> 23 C7H14O
#> 24 C7H8N2O2
#> 25 C7H5NO2
#> 26 C10H19FN2O3
#> 27 C13H24O
#> 28 C13H18N2O2
#> 29 C11H23O3P
#> 30 C16H20
#> 31 C18H33NO2
#> 32 C14H29N7
#> 33 C16H35NO2
#> 34 C17H38P
#> 35 C16H37N2
#> 36 C18H35NO2
#> 37 C6H29N14
#> 38 C19H38P
#> 39 C13H12BClO3
#> 40 C8H11N3O7
#> 41 C9H15N3O2S2
#> 42 C8H12ClN5O3
#> 43 C9H7N7O3
#> 44 C9H18NO3PS2
#> 45 C9H15O9
#> 46 C11H16INO
#> 47 C6H14N5O5P
#> 48 C8H14NO8P
#> 49 C18H26N6O9S3
#> 50 C16H31N4O10PS3
#> 51 C21H31N2O9PS2
#> 52 C20H24N6O9S3
#> 53 C23H26N4O8S2
#> 54 C5H10NO3PS2
#> 55 C7H5N3O2S2
#> 56 C4H6FN3O3S2
#> 57 C4H6F3NO3S
#> 58 C3H5N3O7S
#> 59 C18H35NO2
#> 60 C14H31N7
#> 61 C16H33N4O
#> 62 C14H35N4O
#> 63 C18H35NO2
#> 64 C6H29N14
#> 65 C19H38P
#> 66 C18H35NO2
#> 67 C14H31N7
#> 68 C16H33N4O
#> 69 C14H35N4O
#> 70 C12H11Cl2N3O2
#> 71 C10H13Cl2N3O2
#> 72 C10H16Cl2NO3P
#> 73 C8H18Cl2NO3P
#> 74 C15H13Cl2N
#> 75 C18H35NO2
#> 76 C6H29N14
#> 77 C19H38P
#> 78 C13H18ClNO2
#> 79 C13H14ClN4O
#> 80 C11H16ClN4O
#> 81 C10H16ClN3O4
#> 82 C11H14FN3O3
#> 83 C10H15N3O5
#> 84 C12H17FNO2P
#> 85 C9H18F2NO3P
#> 86 C11H15N4O2
#> 87 C8H14F3N3O3
#> 88 C8H14F2NO2P
#> 89 C10H16NOPSi
#> 90 C11H13FNOP
#> 91 C6H13F2N3O2Si
#> 92 C7H10F3N3O2
#> 93 C13H18ClNO2
#> 94 C8H15F2N3O4
#> 95 C10H19ClFNO3
#> 96 C11H14FN3O3
#> 97 C14H19NO
#> 98 C12H14ClNO
#> 99 C9H15ClFNO2
#> 100 C11H14NO2P
#> adduct rank
#> 1 [M + H]+ 1
#> 2 [M + H]+ 2
#> 3 [M + Na]+ 3
#> 4 [M + Na]+ 4
#> 5 [M + K]+ 5
#> 6 [M + H]+ 1
#> 7 [M + H]+ 2
#> 8 [M + Na]+ 3
#> 9 [M + Na]+ 4
#> 10 [M + K]+ 5
#> 11 [M + H]+ 1
#> 12 [M + H]+ 2
#> 13 [M + H]+ 3
#> 14 [M + H]+ 4
#> 15 [M + Na]+ 5
#> 16 [M + H]+ 1
#> 17 [M + H]+ 2
#> 18 [M + H]+ 3
#> 19 [M + H]+ 4
#> 20 [M + K]+ 5
#> 21 [M + H]+ 1
#> 22 [M + H3N + H]+ 2
#> 23 [M + K]+ 3
#> 24 [M + H]+ 4
#> 25 [M + H3N + H]+ 5
#> 26 [M + H]+ 1
#> 27 [M + K]+ 2
#> 28 [M + H]+ 3
#> 29 [M + H]+ 4
#> 30 [M + Na]+ 5
#> 31 [M + H]+ 1
#> 32 [M + H]+ 2
#> 33 [M + Na]+ 3
#> 34 [M + Na]+ 4
#> 35 [M + K]+ 5
#> 36 [M + H]+ 1
#> 37 [M + H]+ 2
#> 38 [M + H]+ 3
#> 39 [M + Na]+ 1
#> 40 [M + Na]+ 2
#> 41 [M + Na]+ 3
#> 42 [M + Na]+ 4
#> 43 [M + Na]+ 5
#> 44 [M + Na]+ 1
#> 45 [M + K]+ 2
#> 46 [M + H]+ 3
#> 47 [M + K]+ 4
#> 48 [M + Na]+ 5
#> 49 [M + Na]+ 1
#> 50 [M + Na]+ 2
#> 51 [M + K]+ 3
#> 52 [M + H]+ 4
#> 53 [M + K]+ 5
#> 54 [M + H]+ 1
#> 55 [M + H]+ 2
#> 56 [M + H]+ 3
#> 57 [M + Na]+ 4
#> 58 [M + H]+ 5
#> 59 [M + H]+ 1
#> 60 [M + H]+ 2
#> 61 [M + H]+ 3
#> 62 [M + Na]+ 4
#> 63 [M + H]+ 1
#> 64 [M + H]+ 2
#> 65 [M + H]+ 3
#> 66 [M + H]+ 1
#> 67 [M + H]+ 2
#> 68 [M + H]+ 3
#> 69 [M + Na]+ 4
#> 70 [M + H]+ 1
#> 71 [M + Na]+ 2
#> 72 [M + H]+ 3
#> 73 [M + Na]+ 4
#> 74 [M + Na]+ 5
#> 75 [M + H]+ 1
#> 76 [M + H]+ 2
#> 77 [M + H]+ 3
#> 78 [M + Na]+ 1
#> 79 [M + H]+ 2
#> 80 [M + Na]+ 3
#> 81 [M + H]+ 4
#> 82 [M + Na]+ 5
#> 83 [M + H]+ 1
#> 84 [M + H]+ 2
#> 85 [M + H]+ 3
#> 86 [M + Na]+ 4
#> 87 [M + H]+ 5
#> 88 [M + H]+ 1
#> 89 [M + H]+ 2
#> 90 [M + H]+ 3
#> 91 [M + H]+ 4
#> 92 [M + H]+ 5
#> 93 [M + H]+ 1
#> 94 [M + H]+ 2
#> 95 [M + H]+ 3
#> 96 [M + H]+ 4
#> 97 [M + K]+ 5
#> 98 [M + H]+ 1
#> 99 [M + H]+ 2
#> 100 [M + H]+ 3
#> siriusScoreNormalized
#> 1 8.222814e-02
#> 2 8.222814e-02
#> 3 8.222814e-02
#> 4 8.222814e-02
#> 5 8.222814e-02
#> 6 7.231049e-02
#> 7 7.231049e-02
#> 8 7.231049e-02
#> 9 7.231049e-02
#> 10 7.231049e-02
#> 11 8.122791e-01
#> 12 9.484521e-02
#> 13 8.302361e-02
#> 14 6.517148e-03
#> 15 2.036129e-03
#> 16 9.468099e-01
#> 17 5.319014e-02
#> 18 7.593616e-12
#> 19 7.244206e-12
#> 20 1.602132e-12
#> 21 5.000000e-01
#> 22 5.000000e-01
#> 23 2.581802e-08
#> 24 1.751684e-09
#> 25 1.751684e-09
#> 26 9.958532e-01
#> 27 4.078914e-03
#> 28 2.430394e-05
#> 29 2.198486e-05
#> 30 1.128546e-05
#> 31 1.977496e-01
#> 32 1.977496e-01
#> 33 1.977496e-01
#> 34 1.977496e-01
#> 35 1.977496e-01
#> 36 9.928559e-01
#> 37 7.119892e-03
#> 38 2.425273e-05
#> 39 8.921402e-01
#> 40 3.701841e-02
#> 41 1.026673e-02
#> 42 9.089105e-03
#> 43 7.991591e-03
#> 44 5.280432e-01
#> 45 2.297166e-01
#> 46 1.755671e-01
#> 47 2.677341e-02
#> 48 7.315068e-03
#> 49 4.283474e-01
#> 50 2.701445e-01
#> 51 7.726103e-02
#> 52 4.345187e-02
#> 53 2.681164e-02
#> 54 9.672835e-01
#> 55 1.312974e-02
#> 56 1.114546e-02
#> 57 2.348729e-03
#> 58 2.029259e-03
#> 59 2.500000e-01
#> 60 2.500000e-01
#> 61 2.500000e-01
#> 62 2.500000e-01
#> 63 3.333333e-01
#> 64 3.333333e-01
#> 65 3.333333e-01
#> 66 2.500000e-01
#> 67 2.500000e-01
#> 68 2.500000e-01
#> 69 2.500000e-01
#> 70 9.769112e-01
#> 71 1.690992e-02
#> 72 1.280042e-03
#> 73 1.206541e-03
#> 74 1.145444e-03
#> 75 3.333333e-01
#> 76 3.333333e-01
#> 77 3.333333e-01
#> 78 9.739294e-01
#> 79 2.381432e-02
#> 80 2.158903e-03
#> 81 5.714491e-05
#> 82 3.974950e-05
#> 83 9.997910e-01
#> 84 6.673339e-05
#> 85 5.216680e-05
#> 86 3.457424e-05
#> 87 3.394164e-05
#> 88 9.763005e-01
#> 89 1.879689e-02
#> 90 4.879830e-03
#> 91 1.622049e-05
#> 92 5.957077e-06
#> 93 9.854011e-01
#> 94 6.214732e-03
#> 95 4.483593e-03
#> 96 2.590275e-03
#> 97 7.188800e-04
#> 98 9.423414e-01
#> 99 5.363181e-02
#> 100 4.021240e-03
#> siriusScore isotopeScore
#> 1 0.000000 0.000000
#> 2 0.000000 0.000000
#> 3 0.000000 0.000000
#> 4 0.000000 0.000000
#> 5 0.000000 0.000000
#> 6 0.000000 0.000000
#> 7 0.000000 0.000000
#> 8 0.000000 0.000000
#> 9 0.000000 0.000000
#> 10 0.000000 0.000000
#> 11 8.520006 0.000000
#> 12 6.372408 0.000000
#> 13 6.239287 0.000000
#> 14 3.694599 0.000000
#> 15 2.531212 0.000000
#> 16 48.071033 0.000000
#> 17 45.191808 0.000000
#> 18 22.521977 0.000000
#> 19 22.474871 0.000000
#> 20 20.966005 0.000000
#> 21 27.906019 1.966055
#> 22 27.906019 1.966055
#> 23 11.126973 0.000000
#> 24 8.436478 2.462666
#> 25 8.436478 2.462666
#> 26 27.272863 4.595855
#> 27 21.775094 0.000000
#> 28 16.652147 4.558103
#> 29 16.551862 3.699803
#> 30 15.885023 1.145766
#> 31 0.000000 0.000000
#> 32 0.000000 0.000000
#> 33 0.000000 0.000000
#> 34 0.000000 0.000000
#> 35 0.000000 0.000000
#> 36 1.435218 0.000000
#> 37 -3.502475 1.488060
#> 38 -9.184594 0.000000
#> 39 13.475137 0.000000
#> 40 10.292929 0.000000
#> 41 9.010422 0.000000
#> 42 8.888590 0.000000
#> 43 8.759904 0.000000
#> 44 20.649269 5.298210
#> 45 19.816937 3.491782
#> 46 19.548112 2.529954
#> 47 17.667500 3.437534
#> 48 16.370027 2.177361
#> 49 19.791416 9.719789
#> 50 19.330439 10.462670
#> 51 18.078672 9.653318
#> 52 17.503136 9.954285
#> 53 17.020318 7.391106
#> 54 16.613407 5.181199
#> 55 12.313795 2.299407
#> 56 12.149948 5.106717
#> 57 10.592790 4.684342
#> 58 10.446586 4.320071
#> 59 0.000000 0.000000
#> 60 0.000000 0.000000
#> 61 0.000000 0.000000
#> 62 0.000000 0.000000
#> 63 0.000000 0.000000
#> 64 0.000000 0.000000
#> 65 0.000000 0.000000
#> 66 0.000000 0.000000
#> 67 0.000000 0.000000
#> 68 0.000000 0.000000
#> 69 0.000000 0.000000
#> 70 20.181033 11.401897
#> 71 16.124537 9.373567
#> 72 13.543530 11.162029
#> 73 13.484395 10.809551
#> 74 13.432430 7.615923
#> 75 0.000000 0.000000
#> 76 0.000000 0.000000
#> 77 0.000000 0.000000
#> 78 51.148372 5.034061
#> 79 47.437320 4.538336
#> 80 45.036633 6.473512
#> 81 41.404868 5.139461
#> 82 41.041875 1.105920
#> 83 29.277956 3.239972
#> 84 19.663360 1.818560
#> 85 19.417101 2.124648
#> 86 19.005763 3.140810
#> 87 18.987297 1.636000
#> 88 54.550162 2.185135
#> 89 50.600083 1.012402
#> 90 49.251502 1.885489
#> 91 43.544911 2.553124
#> 92 42.543216 1.723650
#> 93 35.131892 6.813786
#> 94 30.065766 3.193495
#> 95 29.739268 8.498871
#> 96 29.190607 1.906369
#> 97 27.908783 0.000000
#> 98 27.422646 8.443987
#> 99 24.556421 8.247907
#> 100 21.965868 2.934373
#> treeScore xcms_fts
#> 1 0.000000 CP001
#> 2 0.000000 CP001
#> 3 0.000000 CP001
#> 4 0.000000 CP001
#> 5 0.000000 CP001
#> 6 0.000000 CP002
#> 7 0.000000 CP002
#> 8 0.000000 CP002
#> 9 0.000000 CP002
#> 10 0.000000 CP002
#> 11 8.520006 CP003
#> 12 6.372408 CP003
#> 13 6.239287 CP003
#> 14 3.694599 CP003
#> 15 2.531212 CP003
#> 16 48.071033 CP004
#> 17 45.191808 CP004
#> 18 22.521977 CP004
#> 19 22.474871 CP004
#> 20 20.966005 CP004
#> 21 25.939964 CP005
#> 22 25.939964 CP005
#> 23 11.126973 CP005
#> 24 5.973812 CP005
#> 25 5.973812 CP005
#> 26 22.677008 CP006
#> 27 21.775094 CP006
#> 28 12.094044 CP006
#> 29 12.852059 CP006
#> 30 14.739257 CP006
#> 31 0.000000 CP007
#> 32 0.000000 CP007
#> 33 0.000000 CP007
#> 34 0.000000 CP007
#> 35 0.000000 CP007
#> 36 1.435218 CP008
#> 37 -4.990535 CP008
#> 38 -9.184594 CP008
#> 39 13.475137 CP011
#> 40 10.292929 CP011
#> 41 9.010422 CP011
#> 42 8.888590 CP011
#> 43 8.759904 CP011
#> 44 15.351059 CP012
#> 45 16.325155 CP012
#> 46 17.018157 CP012
#> 47 14.229966 CP012
#> 48 14.192666 CP012
#> 49 10.071627 CP013
#> 50 8.867769 CP013
#> 51 8.425353 CP013
#> 52 7.548851 CP013
#> 53 9.629211 CP013
#> 54 11.432208 CP014
#> 55 10.014388 CP014
#> 56 7.043231 CP014
#> 57 5.908448 CP014
#> 58 6.126515 CP014
#> 59 0.000000 CP015
#> 60 0.000000 CP015
#> 61 0.000000 CP015
#> 62 0.000000 CP015
#> 63 0.000000 CP016
#> 64 0.000000 CP016
#> 65 0.000000 CP016
#> 66 0.000000 CP017
#> 67 0.000000 CP017
#> 68 0.000000 CP017
#> 69 0.000000 CP017
#> 70 8.779136 CP018
#> 71 6.750971 CP018
#> 72 2.381501 CP018
#> 73 2.674844 CP018
#> 74 5.816507 CP018
#> 75 0.000000 CP019
#> 76 0.000000 CP019
#> 77 0.000000 CP019
#> 78 46.114311 CP022
#> 79 42.898984 CP022
#> 80 38.563121 CP022
#> 81 36.265407 CP022
#> 82 39.935955 CP022
#> 83 26.037984 CP023
#> 84 17.844800 CP023
#> 85 17.292453 CP023
#> 86 15.864953 CP023
#> 87 17.351297 CP023
#> 88 52.365027 CP024
#> 89 49.587680 CP024
#> 90 47.366012 CP024
#> 91 40.991787 CP024
#> 92 40.819566 CP024
#> 93 28.318106 CP025
#> 94 26.872271 CP025
#> 95 21.240397 CP025
#> 96 27.284238 CP025
#> 97 27.908783 CP025
#> 98 18.978658 CP026
#> 99 16.308514 CP026
#> 100 19.031495 CP026
#> sirius_fts
#> 1 819205328622094770
#> 2 819205328622094770
#> 3 819205328622094770
#> 4 819205328622094770
#> 5 819205328622094770
#> 6 819205328718563763
#> 7 819205328718563763
#> 8 819205328718563763
#> 9 819205328718563763
#> 10 819205328718563763
#> 11 819205328735340980
#> 12 819205328735340980
#> 13 819205328735340980
#> 14 819205328735340980
#> 15 819205328735340980
#> 16 819205328781478325
#> 17 819205328781478325
#> 18 819205328781478325
#> 19 819205328781478325
#> 20 819205328781478325
#> 21 819205328798255542
#> 22 819205328798255542
#> 23 819205328798255542
#> 24 819205328798255542
#> 25 819205328798255542
#> 26 819205328810838455
#> 27 819205328810838455
#> 28 819205328810838455
#> 29 819205328810838455
#> 30 819205328810838455
#> 31 819205328831809976
#> 32 819205328831809976
#> 33 819205328831809976
#> 34 819205328831809976
#> 35 819205328831809976
#> 36 819205328844392889
#> 37 819205328844392889
#> 38 819205328844392889
#> 39 819205328886335932
#> 40 819205328886335932
#> 41 819205328886335932
#> 42 819205328886335932
#> 43 819205328886335932
#> 44 819205328903113149
#> 45 819205328903113149
#> 46 819205328903113149
#> 47 819205328903113149
#> 48 819205328903113149
#> 49 819205328919890366
#> 50 819205328919890366
#> 51 819205328919890366
#> 52 819205328919890366
#> 53 819205328919890366
#> 54 819205328932473279
#> 55 819205328932473279
#> 56 819205328932473279
#> 57 819205328932473279
#> 58 819205328932473279
#> 59 819205328970222016
#> 60 819205328970222016
#> 61 819205328970222016
#> 62 819205328970222016
#> 63 819205328982804929
#> 64 819205328982804929
#> 65 819205328982804929
#> 66 819205328995387842
#> 67 819205328995387842
#> 68 819205328995387842
#> 69 819205328995387842
#> 70 819205329012165059
#> 71 819205329012165059
#> 72 819205329012165059
#> 73 819205329012165059
#> 74 819205329012165059
#> 75 819205329028942276
#> 76 819205329028942276
#> 77 819205329028942276
#> 78 819205329058302407
#> 79 819205329058302407
#> 80 819205329058302407
#> 81 819205329058302407
#> 82 819205329058302407
#> 83 819205329066691016
#> 84 819205329066691016
#> 85 819205329066691016
#> 86 819205329066691016
#> 87 819205329066691016
#> 88 819205329075079625
#> 89 819205329075079625
#> 90 819205329075079625
#> 91 819205329075079625
#> 92 819205329075079625
#> 93 819205329079273930
#> 94 819205329079273930
#> 95 819205329079273930
#> 96 819205329079273930
#> 97 819205329079273930
#> 98 819205329087662539
#> 99 819205329087662539
#> 100 819205329087662539
#> [ reached 'max' / getOption("max.print") -- omitted 388 rows ]Structure DBs search results
The following example shows the top two structure annotations for the top five formulas of each feature. This can provide an insightful view into the structural predictions.
finalstructredb <- results(srs,
return.type = "data.frame",
result.type = "structureDb",
topFormula = 5,
topStructure = 2)
head(finalstructredb)
#> formulaId
#> 1 819205523682397402
#> 2 819205523682397403
#> 3 819205523682397404
#> 4 819205523682397405
#> 5 819205523682397406
#> 6 819205528308714745
#> molecularFormula adduct
#> 1 C6H12N6O3 [M + H]+
#> 2 C8H15F3O3 [M + H]+
#> 3 C8H18O5 [M + Na]+
#> 4 C9H14N4O [M + Na]+
#> 5 C6H18N4O2 [M + K]+
#> 6 C10H16O5 [M + H]+
#> rank siriusScoreNormalized
#> 1 1 0.08222814
#> 2 2 0.08222814
#> 3 3 0.08222814
#> 4 4 0.08222814
#> 5 5 0.08222814
#> 6 1 0.07231049
#> siriusScore isotopeScore
#> 1 0 0
#> 2 0 0
#> 3 0 0
#> 4 0 0
#> 5 0 0
#> 6 0 0
#> treeScore xcms_fts
#> 1 0 CP001
#> 2 0 CP001
#> 3 0 CP001
#> 4 0 CP001
#> 5 0 CP001
#> 6 0 CP002
#> sirius_fts rank.x
#> 1 819205328622094770 NA
#> 2 819205328622094770 NA
#> 3 819205328622094770 NA
#> 4 819205328622094770 NA
#> 5 819205328622094770 NA
#> 6 819205328718563763 NA
#> inchiKey smiles
#> 1 <NA> <NA>
#> 2 <NA> <NA>
#> 3 <NA> <NA>
#> 4 <NA> <NA>
#> 5 <NA> <NA>
#> 6 <NA> <NA>
#> structureName xlogP rank.y
#> 1 <NA> NA NA
#> 2 <NA> NA NA
#> 3 <NA> NA NA
#> 4 <NA> NA NA
#> 5 <NA> NA NA
#> 6 <NA> NA NA
#> csiScore tanimotoSimilarity
#> 1 NA NA
#> 2 NA NA
#> 3 NA NA
#> 4 NA NA
#> 5 NA NA
#> 6 NA NA
#> mcesDistToTopHit
#> 1 NA
#> 2 NA
#> 3 NA
#> 4 NA
#> 5 NA
#> 6 NAFor a more visual exploration of the results, you can open the Sirius GUI with the commands below:
Compound class prediction results
To retrieve compound class predictions, use the following code. Below is an example showing all compound annotations with confidence scores above 50% for the top two formulas of each feature.
finalcomp <- results(srs,
return.type = "data.frame",
result.type = "compoundClass",
topFormula = 2)
#> Warning in value[[3L]](cond):
#> Formula:819205523682397402for
#> feature:819205328622094770does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205523682397403for
#> feature:819205328622094770does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205528308714745for
#> feature:819205328718563763does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205528308714746for
#> feature:819205328718563763does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205510843632742for
#> feature:819205328810838455does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205526358363380for
#> feature:819205328831809976does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205526358363381for
#> feature:819205328831809976does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205507509161048for
#> feature:819205328844392889does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205507509161049for
#> feature:819205328844392889does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205516493360273for
#> feature:819205328886335932does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205525842463973for
#> feature:819205328932473279does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205524462537952for
#> feature:819205328970222016does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205524462537953for
#> feature:819205328970222016does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205512961756275for
#> feature:819205328982804929does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205512961756276for
#> feature:819205328982804929does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205522893868246for
#> feature:819205328995387842does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205522893868247for
#> feature:819205328995387842does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205506200538187for
#> feature:819205329012165059does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205490031496201for
#> feature:819205329028942276does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205490031496202for
#> feature:819205329028942276does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205518573735090for
#> feature:819205329066691016does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205488471215096for
#> feature:819205329091856844does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205488471215097for
#> feature:819205329091856844does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205484335631315for
#> feature:819205329096051149does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205484335631316for
#> feature:819205329096051149does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205483341581260for
#> feature:819205329096051150does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205483341581261for
#> feature:819205329096051150does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205521677520079for
#> feature:819205329096051151does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205521677520080for
#> feature:819205329096051151does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205472750963618for
#> feature:819205329108634064does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205472750963619for
#> feature:819205329108634064does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205460440681354for
#> feature:819205329108634065does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205460440681355for
#> feature:819205329108634065does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205543995411756for
#> feature:819205329117022675does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205415444187863for
#> feature:819205329171548630does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205415444187864for
#> feature:819205329171548630does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205450420489077for
#> feature:819205329175742935does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205450420489078for
#> feature:819205329175742935does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205411530902217for
#> feature:819205329175742936does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205411530902218for
#> feature:819205329175742936does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205442145127261for
#> feature:819205329200908763does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205407416289954for
#> feature:819205329230268895does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205407416289955for
#> feature:819205329230268895does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205485380013018for
#> feature:819205329234463201does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205485380013019for
#> feature:819205329234463201does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205488420883441for
#> feature:819205329242851811does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205488420883442for
#> feature:819205329242851811does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205407504370345for
#> feature:819205329247046117does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205407504370346for
#> feature:819205329247046117does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205425044949783for
#> feature:819205329297377770does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205425044949784for
#> feature:819205329297377770does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205423790852872for
#> feature:819205329301572075does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205423790852873for
#> feature:819205329301572075does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205426873666337for
#> feature:819205329318349292does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205426873666338for
#> feature:819205329318349292does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205437749496654for
#> feature:819205329326737902does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205437749496655for
#> feature:819205329326737902does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205538811251985for
#> feature:819205329406429688does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205538811251986for
#> feature:819205329406429688does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205553004776755for
#> feature:819205329427401216does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205419655269118for
#> feature:819205329435789826does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205433840405318for
#> feature:819205329439984132does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205433840405319for
#> feature:819205329439984132does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205430027782954for
#> feature:819205329439984133does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205430027782955for
#> feature:819205329439984133does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205506821295185for
#> feature:819205329444178438does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205506821295186for
#> feature:819205329444178438does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205491142986772for
#> feature:819205329448372744does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205491142986773for
#> feature:819205329448372744does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205479155665850for
#> feature:819205329465149965does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205479155665851for
#> feature:819205329465149965does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205473581435817for
#> feature:819205329481927186does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205473581435818for
#> feature:819205329481927186does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205441662782296for
#> feature:819205329481927187does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205525884407021for
#> feature:819205329490315798does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205487447804908for
#> feature:819205329494510103does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205487447804909for
#> feature:819205329494510103does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205530628164863for
#> feature:819205329494510104does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205530628164864for
#> feature:819205329494510104does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205408141904560for
#> feature:819205329498704409does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205408141904561for
#> feature:819205329498704409does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205421408488197for
#> feature:819205329498704410does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205421408488198for
#> feature:819205329498704410does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205486751550441for
#> feature:819205329498704411does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205486751550442for
#> feature:819205329498704411does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205519664254137for
#> feature:819205329498704412does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205519664254138for
#> feature:819205329498704412does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205514480094335for
#> feature:819205329502898717does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205514480094336for
#> feature:819205329502898717does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205559208152377for
#> feature:819205329502898718does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205559208152378for
#> feature:819205329502898718does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205499330268198for
#> feature:819205329502898719does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205499330268199for
#> feature:819205329502898719does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205487472970734for
#> feature:819205329502898720does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205487472970735for
#> feature:819205329502898720does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205431390931778for
#> feature:819205329511287329does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205431390931779for
#> feature:819205329511287329does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205534767942920for
#> feature:819205329511287330does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205534767942921for
#> feature:819205329511287330does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205446842747754for
#> feature:819205329515481635does
#> not have compound classes
#> information.
#> Warning in value[[3L]](cond):
#> Formula:819205446846942059for
#> feature:819205329515481635does
#> not have compound classes
#> information.
head(finalcomp)
#> formulaId
#> 1 819205523682397402
#> 2 819205523682397403
#> 3 819205528308714745
#> 4 819205528308714746
#> 5 819205520754773183
#> 6 819205520754773183
#> molecularFormula adduct
#> 1 C6H12N6O3 [M + H]+
#> 2 C8H15F3O3 [M + H]+
#> 3 C10H16O5 [M + H]+
#> 4 C6H12N6O3 [M + H]+
#> 5 C9H14FNO4 [M + H]+
#> 6 C9H14FNO4 [M + H]+
#> rank siriusScoreNormalized
#> 1 1 0.08222814
#> 2 2 0.08222814
#> 3 1 0.07231049
#> 4 2 0.07231049
#> 5 1 0.81227913
#> 6 1 0.81227913
#> siriusScore isotopeScore
#> 1 0.000000 0
#> 2 0.000000 0
#> 3 0.000000 0
#> 4 0.000000 0
#> 5 8.520006 0
#> 6 8.520006 0
#> treeScore xcms_fts
#> 1 0.000000 CP001
#> 2 0.000000 CP001
#> 3 0.000000 CP002
#> 4 0.000000 CP002
#> 5 8.520006 CP003
#> 6 8.520006 CP003
#> sirius_fts
#> 1 819205328622094770
#> 2 819205328622094770
#> 3 819205328718563763
#> 4 819205328718563763
#> 5 819205328735340980
#> 6 819205328735340980
#> section type
#> 1 <NA> <NA>
#> 2 <NA> <NA>
#> 3 <NA> <NA>
#> 4 <NA> <NA>
#> 5 npcPathway NPC
#> 6 npcSuperclass NPC
#> level levelIndex
#> 1 <NA> NA
#> 2 <NA> NA
#> 3 <NA> NA
#> 4 <NA> NA
#> 5 PATHWAY 0
#> 6 SUPERCLASS 1
#> name
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 Amino acids and Peptides
#> 6 Small peptides
#> description
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 Pathway: Amino acids and Peptides
#> 6 Superclass: Small peptides
#> id probability index
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 NA NA NA
#> 4 NA NA NA
#> 5 1 0.5644959 1
#> 6 63 0.1956930 63
#> parentId parentName
#> 1 NA <NA>
#> 2 NA <NA>
#> 3 NA <NA>
#> 4 NA <NA>
#> 5 NA <NA>
#> 6 NA <NA>Spectral library matching results
The following code gives you a summary of the best matches:
summaryspectra <- summary(srs, result.type = "spectralDbMatch")
head(summaryspectra)
#> alignedFeatureId
#> 1 819205328622094770
#> 2 819205328718563763
#> 3 819205328735340980
#> 4 819205328781478325
#> 5 819205328798255542
#> 6 819205328810838455
#> spectralMatchCount
#> 1 0
#> 2 0
#> 3 0
#> 4 0
#> 5 0
#> 6 0
#> referenceSpectraCount
#> 1 0
#> 2 0
#> 3 0
#> 4 0
#> 5 0
#> 6 0
#> databaseCompoundCount
#> 1 0
#> 2 0
#> 3 0
#> 4 0
#> 5 0
#> 6 0For detailed results, use the following code:
Fragmentation tree results
Below we show how to get the fragmentation tree for the top2 formula of some feautres. This is quite inefficient at the moment so limit it to a little number of feature. I will improve it.
resulttree <- results(srs,
features = featuresId(srs)[1:5],
return.type = "list",
result.type = "fragTree",
topFormula = 4,
)
head(resulttree)
#> $`819205328622094770`
#> formulaId
#> 1 819205523682397402
#> 2 819205523682397403
#> 3 819205523682397404
#> 4 819205523682397405
#> molecularFormula adduct
#> 1 C6H12N6O3 [M + H]+
#> 2 C8H15F3O3 [M + H]+
#> 3 C8H18O5 [M + Na]+
#> 4 C9H14N4O [M + Na]+
#> rank siriusScoreNormalized
#> 1 1 0.08222814
#> 2 2 0.08222814
#> 3 3 0.08222814
#> 4 4 0.08222814
#> siriusScore isotopeScore
#> 1 0 0
#> 2 0 0
#> 3 0 0
#> 4 0 0
#> treeScore xcms_fts type
#> 1 0 CP001 fragments
#> 2 0 CP001 fragments
#> 3 0 CP001 fragments
#> 4 0 CP001 fragments
#> fragmentId
#> 1 0
#> 2 0
#> 3 0
#> 4 0
#> molecularFormula_fragment
#> 1 C6H12N6O3
#> 2 C8H15F3O3
#> 3 C8H18O5
#> 4 C9H14N4O
#> adduct_fragment
#> 1 [M + H]+
#> 2 [M + H]+
#> 3 [M + Na]+
#> 4 [M + Na]+
#> massDeviationDa
#> 1 0
#> 2 0
#> 3 0
#> 4 0
#> massDeviationPpm score
#> 1 0 2.0000000
#> 2 0 0.3905621
#> 3 0 4.5000000
#> 4 0 2.0000000
#> intensity mz
#> 1 0 217.1042
#> 2 0 217.1042
#> 3 0 217.1042
#> 4 0 217.1042
#>
#> $`819205328718563763`
#> formulaId
#> 1 819205528308714745
#> 2 819205528308714746
#> 3 819205528308714747
#> 4 819205528308714748
#> molecularFormula adduct
#> 1 C10H16O5 [M + H]+
#> 2 C6H12N6O3 [M + H]+
#> 3 C8H18O5 [M + Na]+
#> 4 C9H14N4O [M + Na]+
#> rank siriusScoreNormalized
#> 1 1 0.07231049
#> 2 2 0.07231049
#> 3 3 0.07231049
#> 4 4 0.07231049
#> siriusScore isotopeScore
#> 1 0 0
#> 2 0 0
#> 3 0 0
#> 4 0 0
#> treeScore xcms_fts type
#> 1 0 CP002 fragments
#> 2 0 CP002 fragments
#> 3 0 CP002 fragments
#> 4 0 CP002 fragments
#> fragmentId
#> 1 0
#> 2 0
#> 3 0
#> 4 0
#> molecularFormula_fragment
#> 1 C10H16O5
#> 2 C6H12N6O3
#> 3 C8H18O5
#> 4 C9H14N4O
#> adduct_fragment
#> 1 [M + H]+
#> 2 [M + H]+
#> 3 [M + Na]+
#> 4 [M + Na]+
#> massDeviationDa
#> 1 0
#> 2 0
#> 3 0
#> 4 0
#> massDeviationPpm score
#> 1 0 4.5
#> 2 0 2.0
#> 3 0 4.5
#> 4 0 2.0
#> intensity mz
#> 1 0 217.1055
#> 2 0 217.1055
#> 3 0 217.1055
#> 4 0 217.1055
#>
#> $`819205328735340980`
#> formulaId
#> 1 819205520754773183
#> 2 819205520754773183
#> 3 819205520754773183
#> 4 819205520754773183
#> 5 819205520754773183
#> 6 819205520754773184
#> 7 819205520754773184
#> 8 819205520754773184
#> 9 819205520754773184
#> 10 819205520754773184
#> 11 819205520754773185
#> 12 819205520754773185
#> 13 819205520754773185
#> 14 819205520754773186
#> 15 819205520754773186
#> 16 819205520754773186
#> 17 819205520754773186
#> 18 819205520754773186
#> 19 819205520754773186
#> 20 819205520754773186
#> molecularFormula adduct
#> 1 C9H14FNO4 [M + H]+
#> 2 C9H14FNO4 [M + H]+
#> 3 C9H14FNO4 [M + H]+
#> 4 C9H14FNO4 [M + H]+
#> 5 C9H14FNO4 [M + H]+
#> 6 C10H10FN5 [M + H]+
#> 7 C10H10FN5 [M + H]+
#> 8 C10H10FN5 [M + H]+
#> 9 C10H10FN5 [M + H]+
#> 10 C10H10FN5 [M + H]+
#> 11 C12H13NO3 [M + H]+
#> 12 C12H13NO3 [M + H]+
#> 13 C12H13NO3 [M + H]+
#> 14 C9H15F2NOSi [M + H]+
#> 15 C9H15F2NOSi [M + H]+
#> 16 C9H15F2NOSi [M + H]+
#> 17 C9H15F2NOSi [M + H]+
#> 18 C9H15F2NOSi [M + H]+
#> 19 C9H15F2NOSi [M + H]+
#> 20 C9H15F2NOSi [M + H]+
#> rank siriusScoreNormalized
#> 1 1 0.812279133
#> 2 1 0.812279133
#> 3 1 0.812279133
#> 4 1 0.812279133
#> 5 1 0.812279133
#> 6 2 0.094845210
#> 7 2 0.094845210
#> 8 2 0.094845210
#> 9 2 0.094845210
#> 10 2 0.094845210
#> 11 3 0.083023608
#> 12 3 0.083023608
#> 13 3 0.083023608
#> 14 4 0.006517148
#> 15 4 0.006517148
#> 16 4 0.006517148
#> 17 4 0.006517148
#> 18 4 0.006517148
#> 19 4 0.006517148
#> 20 4 0.006517148
#> siriusScore isotopeScore
#> 1 8.520006 0
#> 2 8.520006 0
#> 3 8.520006 0
#> 4 8.520006 0
#> 5 8.520006 0
#> 6 6.372408 0
#> 7 6.372408 0
#> 8 6.372408 0
#> 9 6.372408 0
#> 10 6.372408 0
#> 11 6.239287 0
#> 12 6.239287 0
#> 13 6.239287 0
#> 14 3.694599 0
#> 15 3.694599 0
#> 16 3.694599 0
#> 17 3.694599 0
#> 18 3.694599 0
#> 19 3.694599 0
#> 20 3.694599 0
#> treeScore xcms_fts
#> 1 8.520006 CP003
#> 2 8.520006 CP003
#> 3 8.520006 CP003
#> 4 8.520006 CP003
#> 5 8.520006 CP003
#> 6 6.372408 CP003
#> 7 6.372408 CP003
#> 8 6.372408 CP003
#> 9 6.372408 CP003
#> 10 6.372408 CP003
#> 11 6.239287 CP003
#> 12 6.239287 CP003
#> 13 6.239287 CP003
#> 14 3.694599 CP003
#> 15 3.694599 CP003
#> 16 3.694599 CP003
#> 17 3.694599 CP003
#> 18 3.694599 CP003
#> 19 3.694599 CP003
#> 20 3.694599 CP003
#> type fragmentId
#> 1 fragments 0
#> 2 fragments 1
#> 3 fragments 2
#> 4 losses NA
#> 5 losses NA
#> 6 fragments 0
#> 7 fragments 1
#> 8 fragments 2
#> 9 losses NA
#> 10 losses NA
#> 11 fragments 0
#> 12 fragments 1
#> 13 losses NA
#> 14 fragments 0
#> 15 fragments 1
#> 16 fragments 2
#> 17 fragments 3
#> 18 losses NA
#> 19 losses NA
#> 20 losses NA
#> molecularFormula_fragment
#> 1 C9H14FNO4
#> 2 C8H10FNO4
#> 3 C7H10FNO
#> 4 CH4
#> 5 C2H4O3
#> 6 C10H10FN5
#> 7 C9H6FN5
#> 8 C10H9N
#> 9 CH4
#> 10 FHN4
#> 11 C12H13NO3
#> 12 C10H9N
#> 13 C2H4O3
#> 14 C9H15F2NOSi
#> 15 C9H11F2N
#> 16 C8H10F2
#> 17 C7H10FNO
#> 18 H4OSi
#> 19 CHN
#> 20 C2H5FSi
#> adduct_fragment
#> 1 [M + H]+
#> 2 [M + H]+
#> 3 [M + H]+
#> 4 <NA>
#> 5 <NA>
#> 6 [M + H]+
#> 7 [M + H]+
#> 8 [M + H]+
#> 9 <NA>
#> 10 <NA>
#> 11 [M + H]+
#> 12 [M + H]+
#> 13 <NA>
#> 14 [M + H]+
#> 15 [M + H]+
#> 16 [M + H]+
#> 17 [M + H]+
#> 18 <NA>
#> 19 <NA>
#> 20 <NA>
#> massDeviationDa
#> 1 -1.537622e-04
#> 2 1.742679e-03
#> 3 -1.047030e-03
#> 4 NA
#> 5 NA
#> 6 -1.491154e-03
#> 7 4.052873e-04
#> 8 9.584194e-05
#> 9 NA
#> 10 NA
#> 11 9.891098e-04
#> 12 9.584194e-05
#> 13 NA
#> 14 1.435316e-03
#> 15 -3.977714e-04
#> 16 7.508944e-04
#> 17 -1.047030e-03
#> 18 NA
#> 19 NA
#> 20 NA
#> massDeviationPpm score
#> 1 -0.6986085 -1.6667446
#> 2 8.5396820 4.6780651
#> 3 -7.2669609 6.9231516
#> 4 NA 4.7569242
#> 5 NA 5.4298262
#> 6 -6.7749616 -2.3064100
#> 7 1.9860364 5.0592344
#> 8 0.6651955 5.6315752
#> 9 NA 5.1380935
#> 10 NA 3.5407245
#> 11 4.4939557 0.5740459
#> 12 0.6651955 7.1585663
#> 13 NA 5.6652409
#> 14 6.5212635 -2.8837861
#> 15 -2.3113771 3.5947147
#> 16 5.1756162 3.8008662
#> 17 -7.2669609 3.3961606
#> 18 NA 1.8183825
#> 19 NA 4.5317564
#> 20 NA 0.2282458
#> intensity mz
#> 1 1.00000000 220.0978
#> 2 0.07443315 204.0684
#> 3 0.06788801 144.0809
#> 4 NA NA
#> 5 NA NA
#> 6 1.00000000 220.0978
#> 7 0.07443315 204.0684
#> 8 0.06788801 144.0809
#> 9 NA NA
#> 10 NA NA
#> 11 1.00000000 220.0978
#> 12 0.06788801 144.0809
#> 13 NA NA
#> 14 1.00000000 220.0978
#> 15 0.11297021 172.0928
#> 16 0.11707711 145.0831
#> 17 0.06788801 144.0809
#> 18 NA NA
#> 19 NA NA
#> 20 NA NA
#> sourceFragmentIdx
#> 1 NA
#> 2 NA
#> 3 NA
#> 4 0
#> 5 0
#> 6 NA
#> 7 NA
#> 8 NA
#> 9 0
#> 10 0
#> 11 NA
#> 12 NA
#> 13 0
#> 14 NA
#> 15 NA
#> 16 NA
#> 17 NA
#> 18 0
#> 19 1
#> 20 0
#> targetFragmentIdx
#> 1 NA
#> 2 NA
#> 3 NA
#> 4 1
#> 5 2
#> 6 NA
#> 7 NA
#> 8 NA
#> 9 1
#> 10 2
#> 11 NA
#> 12 NA
#> 13 1
#> 14 NA
#> 15 NA
#> 16 NA
#> 17 NA
#> 18 1
#> 19 2
#> 20 3
#>
#> $`819205328781478325`
#> formulaId
#> 1 819205514274573431
#> 2 819205514274573431
#> 3 819205514274573431
#> 4 819205514274573431
#> 5 819205514274573431
#> 6 819205514274573431
#> 7 819205514274573431
#> 8 819205514274573431
#> 9 819205514274573431
#> 10 819205514274573431
#> 11 819205514274573431
#> 12 819205514274573431
#> 13 819205514274573431
#> 14 819205514274573431
#> 15 819205514274573431
#> 16 819205514274573431
#> 17 819205514274573431
#> 18 819205514274573431
#> 19 819205514274573431
#> 20 819205514274573431
#> 21 819205514274573431
#> 22 819205514274573431
#> 23 819205514274573431
#> 24 819205514274573432
#> 25 819205514274573432
#> 26 819205514274573432
#> 27 819205514274573432
#> 28 819205514274573432
#> 29 819205514274573432
#> 30 819205514274573432
#> 31 819205514274573432
#> 32 819205514274573432
#> 33 819205514274573432
#> 34 819205514274573432
#> 35 819205514274573432
#> 36 819205514274573432
#> 37 819205514274573432
#> 38 819205514274573432
#> 39 819205514274573432
#> 40 819205514274573432
#> 41 819205514274573432
#> 42 819205514274573432
#> 43 819205514274573432
#> 44 819205514274573432
#> 45 819205514274573433
#> 46 819205514274573433
#> 47 819205514274573433
#> 48 819205514274573433
#> 49 819205514274573433
#> 50 819205514274573433
#> molecularFormula adduct
#> 1 C12H14N2S [M + H]+
#> 2 C12H14N2S [M + H]+
#> 3 C12H14N2S [M + H]+
#> 4 C12H14N2S [M + H]+
#> 5 C12H14N2S [M + H]+
#> 6 C12H14N2S [M + H]+
#> 7 C12H14N2S [M + H]+
#> 8 C12H14N2S [M + H]+
#> 9 C12H14N2S [M + H]+
#> 10 C12H14N2S [M + H]+
#> 11 C12H14N2S [M + H]+
#> 12 C12H14N2S [M + H]+
#> 13 C12H14N2S [M + H]+
#> 14 C12H14N2S [M + H]+
#> 15 C12H14N2S [M + H]+
#> 16 C12H14N2S [M + H]+
#> 17 C12H14N2S [M + H]+
#> 18 C12H14N2S [M + H]+
#> 19 C12H14N2S [M + H]+
#> 20 C12H14N2S [M + H]+
#> 21 C12H14N2S [M + H]+
#> 22 C12H14N2S [M + H]+
#> 23 C12H14N2S [M + H]+
#> 24 C6H13F3N2O3 [M + H]+
#> 25 C6H13F3N2O3 [M + H]+
#> 26 C6H13F3N2O3 [M + H]+
#> 27 C6H13F3N2O3 [M + H]+
#> 28 C6H13F3N2O3 [M + H]+
#> 29 C6H13F3N2O3 [M + H]+
#> 30 C6H13F3N2O3 [M + H]+
#> 31 C6H13F3N2O3 [M + H]+
#> 32 C6H13F3N2O3 [M + H]+
#> 33 C6H13F3N2O3 [M + H]+
#> 34 C6H13F3N2O3 [M + H]+
#> 35 C6H13F3N2O3 [M + H]+
#> 36 C6H13F3N2O3 [M + H]+
#> 37 C6H13F3N2O3 [M + H]+
#> 38 C6H13F3N2O3 [M + H]+
#> 39 C6H13F3N2O3 [M + H]+
#> 40 C6H13F3N2O3 [M + H]+
#> 41 C6H13F3N2O3 [M + H]+
#> 42 C6H13F3N2O3 [M + H]+
#> 43 C6H13F3N2O3 [M + H]+
#> 44 C6H13F3N2O3 [M + H]+
#> 45 C11H16ClFO [M + H]+
#> 46 C11H16ClFO [M + H]+
#> 47 C11H16ClFO [M + H]+
#> 48 C11H16ClFO [M + H]+
#> 49 C11H16ClFO [M + H]+
#> 50 C11H16ClFO [M + H]+
#> rank siriusScoreNormalized
#> 1 1 9.468099e-01
#> 2 1 9.468099e-01
#> 3 1 9.468099e-01
#> 4 1 9.468099e-01
#> 5 1 9.468099e-01
#> 6 1 9.468099e-01
#> 7 1 9.468099e-01
#> 8 1 9.468099e-01
#> 9 1 9.468099e-01
#> 10 1 9.468099e-01
#> 11 1 9.468099e-01
#> 12 1 9.468099e-01
#> 13 1 9.468099e-01
#> 14 1 9.468099e-01
#> 15 1 9.468099e-01
#> 16 1 9.468099e-01
#> 17 1 9.468099e-01
#> 18 1 9.468099e-01
#> 19 1 9.468099e-01
#> 20 1 9.468099e-01
#> 21 1 9.468099e-01
#> 22 1 9.468099e-01
#> 23 1 9.468099e-01
#> 24 2 5.319014e-02
#> 25 2 5.319014e-02
#> 26 2 5.319014e-02
#> 27 2 5.319014e-02
#> 28 2 5.319014e-02
#> 29 2 5.319014e-02
#> 30 2 5.319014e-02
#> 31 2 5.319014e-02
#> 32 2 5.319014e-02
#> 33 2 5.319014e-02
#> 34 2 5.319014e-02
#> 35 2 5.319014e-02
#> 36 2 5.319014e-02
#> 37 2 5.319014e-02
#> 38 2 5.319014e-02
#> 39 2 5.319014e-02
#> 40 2 5.319014e-02
#> 41 2 5.319014e-02
#> 42 2 5.319014e-02
#> 43 2 5.319014e-02
#> 44 2 5.319014e-02
#> 45 3 7.593616e-12
#> 46 3 7.593616e-12
#> 47 3 7.593616e-12
#> 48 3 7.593616e-12
#> 49 3 7.593616e-12
#> 50 3 7.593616e-12
#> siriusScore isotopeScore
#> 1 48.07103 0
#> 2 48.07103 0
#> 3 48.07103 0
#> 4 48.07103 0
#> 5 48.07103 0
#> 6 48.07103 0
#> 7 48.07103 0
#> 8 48.07103 0
#> 9 48.07103 0
#> 10 48.07103 0
#> 11 48.07103 0
#> 12 48.07103 0
#> 13 48.07103 0
#> 14 48.07103 0
#> 15 48.07103 0
#> 16 48.07103 0
#> 17 48.07103 0
#> 18 48.07103 0
#> 19 48.07103 0
#> 20 48.07103 0
#> 21 48.07103 0
#> 22 48.07103 0
#> 23 48.07103 0
#> 24 45.19181 0
#> 25 45.19181 0
#> 26 45.19181 0
#> 27 45.19181 0
#> 28 45.19181 0
#> 29 45.19181 0
#> 30 45.19181 0
#> 31 45.19181 0
#> 32 45.19181 0
#> 33 45.19181 0
#> 34 45.19181 0
#> 35 45.19181 0
#> 36 45.19181 0
#> 37 45.19181 0
#> 38 45.19181 0
#> 39 45.19181 0
#> 40 45.19181 0
#> 41 45.19181 0
#> 42 45.19181 0
#> 43 45.19181 0
#> 44 45.19181 0
#> 45 22.52198 0
#> 46 22.52198 0
#> 47 22.52198 0
#> 48 22.52198 0
#> 49 22.52198 0
#> 50 22.52198 0
#> treeScore xcms_fts
#> 1 48.07103 CP004
#> 2 48.07103 CP004
#> 3 48.07103 CP004
#> 4 48.07103 CP004
#> 5 48.07103 CP004
#> 6 48.07103 CP004
#> 7 48.07103 CP004
#> 8 48.07103 CP004
#> 9 48.07103 CP004
#> 10 48.07103 CP004
#> 11 48.07103 CP004
#> 12 48.07103 CP004
#> 13 48.07103 CP004
#> 14 48.07103 CP004
#> 15 48.07103 CP004
#> 16 48.07103 CP004
#> 17 48.07103 CP004
#> 18 48.07103 CP004
#> 19 48.07103 CP004
#> 20 48.07103 CP004
#> 21 48.07103 CP004
#> 22 48.07103 CP004
#> 23 48.07103 CP004
#> 24 45.19181 CP004
#> 25 45.19181 CP004
#> 26 45.19181 CP004
#> 27 45.19181 CP004
#> 28 45.19181 CP004
#> 29 45.19181 CP004
#> 30 45.19181 CP004
#> 31 45.19181 CP004
#> 32 45.19181 CP004
#> 33 45.19181 CP004
#> 34 45.19181 CP004
#> 35 45.19181 CP004
#> 36 45.19181 CP004
#> 37 45.19181 CP004
#> 38 45.19181 CP004
#> 39 45.19181 CP004
#> 40 45.19181 CP004
#> 41 45.19181 CP004
#> 42 45.19181 CP004
#> 43 45.19181 CP004
#> 44 45.19181 CP004
#> 45 22.52198 CP004
#> 46 22.52198 CP004
#> 47 22.52198 CP004
#> 48 22.52198 CP004
#> 49 22.52198 CP004
#> 50 22.52198 CP004
#> type fragmentId
#> 1 fragments 0
#> 2 fragments 1
#> 3 fragments 2
#> 4 fragments 3
#> 5 fragments 4
#> 6 fragments 5
#> 7 fragments 6
#> 8 fragments 7
#> 9 fragments 8
#> 10 fragments 9
#> 11 fragments 10
#> 12 fragments 11
#> 13 losses NA
#> 14 losses NA
#> 15 losses NA
#> 16 losses NA
#> 17 losses NA
#> 18 losses NA
#> 19 losses NA
#> 20 losses NA
#> 21 losses NA
#> 22 losses NA
#> 23 losses NA
#> 24 fragments 0
#> 25 fragments 1
#> 26 fragments 2
#> 27 fragments 3
#> 28 fragments 4
#> 29 fragments 5
#> 30 fragments 6
#> 31 fragments 7
#> 32 fragments 8
#> 33 fragments 9
#> 34 fragments 10
#> 35 losses NA
#> 36 losses NA
#> 37 losses NA
#> 38 losses NA
#> 39 losses NA
#> 40 losses NA
#> 41 losses NA
#> 42 losses NA
#> 43 losses NA
#> 44 losses NA
#> 45 fragments 0
#> 46 fragments 1
#> 47 fragments 2
#> 48 fragments 3
#> 49 fragments 4
#> 50 fragments 5
#> molecularFormula_fragment
#> 1 C12H14N2S
#> 2 C11H11N2S
#> 3 C11H10N2S
#> 4 C10H8N2S
#> 5 C11H10N2
#> 6 C10H7N2
#> 7 C10H9N
#> 8 C10H8N
#> 9 C9H8N
#> 10 C9H7N
#> 11 C8H9N
#> 12 C8H8
#> 13 CH3
#> 14 CH4
#> 15 CH3
#> 16 S
#> 17 CH3
#> 18 CHN
#> 19 CH3NS
#> 20 C2H3NS
#> 21 CHNS
#> 22 C3HN
#> 23 C2HN
#> 24 C6H13F3N2O3
#> 25 C5H10F3N2O3
#> 26 C5H9F3N2O3
#> 27 C4H7F3N2O3
#> 28 C5H12F2N2O2
#> 29 C4H9F2N2O2
#> 30 C4H11F2NO2
#> 31 C4H10F2NO2
#> 32 C3H9F2NO2
#> 33 C5H10FNO
#> 34 C5H9FO
#> 35 CH3
#> 36 CH4
#> 37 CH3
#> 38 CHFO
#> 39 CH3
#> 40 CHN
#> 41 H
#> 42 C2H3N
#> 43 FH2NO
#> 44 FH3N2O
#> 45 C11H16ClFO
#> 46 C10H13ClFO
#> 47 C10H12ClFO
#> 48 C9H10ClFO
#> 49 C10H15Cl
#> 50 C9H12Cl
#> adduct_fragment
#> 1 [M + H]+
#> 2 [M + H]+
#> 3 [M + H]+
#> 4 [M + H]+
#> 5 [M + H]+
#> 6 [M + H]+
#> 7 [M + H]+
#> 8 [M + H]+
#> 9 [M + H]+
#> 10 [M + H]+
#> 11 [M + H]+
#> 12 [M + H]+
#> 13 <NA>
#> 14 <NA>
#> 15 <NA>
#> 16 <NA>
#> 17 <NA>
#> 18 <NA>
#> 19 <NA>
#> 20 <NA>
#> 21 <NA>
#> 22 <NA>
#> 23 <NA>
#> 24 [M + H]+
#> 25 [M + H]+
#> 26 [M + H]+
#> 27 [M + H]+
#> 28 [M + H]+
#> 29 [M + H]+
#> 30 [M + H]+
#> 31 [M + H]+
#> 32 [M + H]+
#> 33 [M + H]+
#> 34 [M + H]+
#> 35 <NA>
#> 36 <NA>
#> 37 <NA>
#> 38 <NA>
#> 39 <NA>
#> 40 <NA>
#> 41 <NA>
#> 42 <NA>
#> 43 <NA>
#> 44 <NA>
#> 45 [M + H]+
#> 46 [M + H]+
#> 47 [M + H]+
#> 48 [M + H]+
#> 49 [M + H]+
#> 50 [M + H]+
#> massDeviationDa
#> 1 0.0012523177
#> 2 0.0004354215
#> 3 0.0010277875
#> 4 0.0006408642
#> 5 0.0013885824
#> 6 0.0010447087
#> 7 0.0011029220
#> 8 0.0006576903
#> 9 0.0011307128
#> 10 0.0006549636
#> 11 0.0009884811
#> 12 0.0009164438
#> 13 NA
#> 14 NA
#> 15 NA
#> 16 NA
#> 17 NA
#> 18 NA
#> 19 NA
#> 20 NA
#> 21 NA
#> 22 NA
#> 23 NA
#> 24 0.0011948297
#> 25 0.0003779335
#> 26 0.0009702995
#> 27 0.0005833762
#> 28 -0.0008971616
#> 29 -0.0012410353
#> 30 -0.0011828220
#> 31 -0.0016280537
#> 32 -0.0016307804
#> 33 -0.0001543909
#> 34 -0.0002264282
#> 35 NA
#> 36 NA
#> 37 NA
#> 38 NA
#> 39 NA
#> 40 NA
#> 41 NA
#> 42 NA
#> 43 NA
#> 44 NA
#> 45 0.0016507337
#> 46 0.0008338375
#> 47 0.0014262035
#> 48 0.0010392802
#> 49 -0.0004412576
#> 50 -0.0007851313
#> massDeviationPpm
#> 1 5.715832
#> 2 2.133666
#> 3 5.061378
#> 4 3.389942
#> 5 8.115948
#> 6 6.693879
#> 7 7.654828
#> 8 4.596867
#> 9 8.626517
#> 10 5.035633
#> 11 8.231734
#> 12 8.722155
#> 13 NA
#> 14 NA
#> 15 NA
#> 16 NA
#> 17 NA
#> 18 NA
#> 19 NA
#> 20 NA
#> 21 NA
#> 22 NA
#> 23 NA
#> 24 5.453445
#> 25 1.851961
#> 26 4.778276
#> 27 3.085851
#> 28 -5.243705
#> 29 -7.951825
#> 30 -8.209374
#> 31 -11.379133
#> 32 -12.538121
#> 33 -1.285715
#> 34 -2.155006
#> 35 NA
#> 36 NA
#> 37 NA
#> 38 NA
#> 39 NA
#> 40 NA
#> 41 NA
#> 42 NA
#> 43 NA
#> 44 NA
#> 45 7.534284
#> 46 4.085996
#> 47 7.023392
#> 48 5.497419
#> 49 -2.579050
#> 50 -5.030660
#> score intensity
#> 1 -0.1757686 0.827676377
#> 2 3.1078620 0.431772302
#> 3 2.7937670 0.380906223
#> 4 0.5219581 0.006316214
#> 5 11.8173194 1.000000000
#> 6 2.6962436 0.133101421
#> 7 6.3838806 0.923662249
#> 8 3.5974360 0.299314154
#> 9 1.3829304 0.006476616
#> 10 3.9145318 0.355810157
#> 11 3.0512030 0.129069092
#> 12 3.5663203 0.131285802
#> 13 4.8202179 NA
#> 14 4.1997289 NA
#> 15 2.5862251 NA
#> 16 12.4868807 NA
#> 17 4.6927471 NA
#> 18 7.6792456 NA
#> 19 2.8620467 NA
#> 20 0.1024434 NA
#> 21 3.3115045 NA
#> 22 2.4045278 NA
#> 23 3.1012343 NA
#> 24 -0.1446987 0.827676377
#> 25 3.5264115 0.431772302
#> 26 3.2153014 0.380906223
#> 27 0.9418298 0.006316214
#> 28 11.9640250 1.000000000
#> 29 2.6376497 0.133101421
#> 30 6.3600354 0.923662249
#> 31 3.3074749 0.299314154
#> 32 3.6229368 0.355810157
#> 33 3.2575522 0.129069092
#> 34 3.4038030 0.131285802
#> 35 5.2387673 NA
#> 36 4.6212633 NA
#> 37 3.0060968 NA
#> 38 11.1004357 NA
#> 39 4.6341531 NA
#> 40 7.6554004 NA
#> 41 1.5082927 NA
#> 42 2.8564656 NA
#> 43 2.4062170 NA
#> 44 2.3094150 NA
#> 45 -21.0147369 0.827676377
#> 46 5.4151131 0.431772302
#> 47 5.0797026 0.380906223
#> 48 2.8195129 0.006316214
#> 49 14.4056915 1.000000000
#> 50 5.1986069 0.133101421
#> mz sourceFragmentIdx
#> 1 219.0963 NA
#> 2 204.0720 NA
#> 3 203.0648 NA
#> 4 189.0487 NA
#> 5 171.0931 NA
#> 6 156.0692 NA
#> 7 144.0819 NA
#> 8 143.0736 NA
#> 9 131.0741 NA
#> 10 130.0658 NA
#> 11 120.0818 NA
#> 12 105.0708 NA
#> 13 NA 0
#> 14 NA 0
#> 15 NA 1
#> 16 NA 2
#> 17 NA 4
#> 18 NA 4
#> 19 NA 1
#> 20 NA 1
#> 21 NA 3
#> 22 NA 4
#> 23 NA 6
#> 24 219.0963 NA
#> 25 204.0720 NA
#> 26 203.0648 NA
#> 27 189.0487 NA
#> 28 171.0931 NA
#> 29 156.0692 NA
#> 30 144.0819 NA
#> 31 143.0736 NA
#> 32 130.0658 NA
#> 33 120.0818 NA
#> 34 105.0708 NA
#> 35 NA 0
#> 36 NA 0
#> 37 NA 1
#> 38 NA 0
#> 39 NA 4
#> 40 NA 4
#> 41 NA 6
#> 42 NA 4
#> 43 NA 4
#> 44 NA 4
#> 45 219.0963 NA
#> 46 204.0720 NA
#> 47 203.0648 NA
#> 48 189.0487 NA
#> 49 171.0931 NA
#> 50 156.0692 NA
#> targetFragmentIdx
#> 1 NA
#> 2 NA
#> 3 NA
#> 4 NA
#> 5 NA
#> 6 NA
#> 7 NA
#> 8 NA
#> 9 NA
#> 10 NA
#> 11 NA
#> 12 NA
#> 13 1
#> 14 2
#> 15 3
#> 16 4
#> 17 5
#> 18 6
#> 19 7
#> 20 8
#> 21 9
#> 22 10
#> 23 11
#> 24 NA
#> 25 NA
#> 26 NA
#> 27 NA
#> 28 NA
#> 29 NA
#> 30 NA
#> 31 NA
#> 32 NA
#> 33 NA
#> 34 NA
#> 35 1
#> 36 2
#> 37 3
#> 38 4
#> 39 5
#> 40 6
#> 41 7
#> 42 8
#> 43 9
#> 44 10
#> 45 NA
#> 46 NA
#> 47 NA
#> 48 NA
#> 49 NA
#> 50 NA
#> [ reached 'max' / getOption("max.print") -- omitted 20 rows ]
#>
#> $`819205328798255542`
#> formulaId
#> 1 819205517835537576
#> 2 819205517835537576
#> 3 819205517835537576
#> 4 819205517835537576
#> 5 819205517835537576
#> 6 819205517835537576
#> 7 819205517835537576
#> 8 819205517835537576
#> 9 819205517835537576
#> 10 819205517835537576
#> 11 819205517835537576
#> 12 819205517835537576
#> 13 819205517835537576
#> 14 819205517835537577
#> 15 819205517835537577
#> 16 819205517835537577
#> 17 819205517835537577
#> 18 819205517835537577
#> 19 819205517835537577
#> 20 819205517835537577
#> 21 819205517835537577
#> 22 819205517835537577
#> 23 819205517835537577
#> 24 819205517835537577
#> 25 819205517835537578
#> 26 819205517835537578
#> 27 819205517835537578
#> 28 819205517835537579
#> 29 819205517835537579
#> 30 819205517835537579
#> molecularFormula
#> 1 C4H9FN2O3
#> 2 C4H9FN2O3
#> 3 C4H9FN2O3
#> 4 C4H9FN2O3
#> 5 C4H9FN2O3
#> 6 C4H9FN2O3
#> 7 C4H9FN2O3
#> 8 C4H9FN2O3
#> 9 C4H9FN2O3
#> 10 C4H9FN2O3
#> 11 C4H9FN2O3
#> 12 C4H9FN2O3
#> 13 C4H9FN2O3
#> 14 C4H6FNO3
#> 15 C4H6FNO3
#> 16 C4H6FNO3
#> 17 C4H6FNO3
#> 18 C4H6FNO3
#> 19 C4H6FNO3
#> 20 C4H6FNO3
#> 21 C4H6FNO3
#> 22 C4H6FNO3
#> 23 C4H6FNO3
#> 24 C4H6FNO3
#> 25 C7H14O
#> 26 C7H14O
#> 27 C7H14O
#> 28 C7H8N2O2
#> 29 C7H8N2O2
#> 30 C7H8N2O2
#> adduct rank
#> 1 [M + H]+ 1
#> 2 [M + H]+ 1
#> 3 [M + H]+ 1
#> 4 [M + H]+ 1
#> 5 [M + H]+ 1
#> 6 [M + H]+ 1
#> 7 [M + H]+ 1
#> 8 [M + H]+ 1
#> 9 [M + H]+ 1
#> 10 [M + H]+ 1
#> 11 [M + H]+ 1
#> 12 [M + H]+ 1
#> 13 [M + H]+ 1
#> 14 [M + H3N + H]+ 2
#> 15 [M + H3N + H]+ 2
#> 16 [M + H3N + H]+ 2
#> 17 [M + H3N + H]+ 2
#> 18 [M + H3N + H]+ 2
#> 19 [M + H3N + H]+ 2
#> 20 [M + H3N + H]+ 2
#> 21 [M + H3N + H]+ 2
#> 22 [M + H3N + H]+ 2
#> 23 [M + H3N + H]+ 2
#> 24 [M + H3N + H]+ 2
#> 25 [M + K]+ 3
#> 26 [M + K]+ 3
#> 27 [M + K]+ 3
#> 28 [M + H]+ 4
#> 29 [M + H]+ 4
#> 30 [M + H]+ 4
#> siriusScoreNormalized
#> 1 5.000000e-01
#> 2 5.000000e-01
#> 3 5.000000e-01
#> 4 5.000000e-01
#> 5 5.000000e-01
#> 6 5.000000e-01
#> 7 5.000000e-01
#> 8 5.000000e-01
#> 9 5.000000e-01
#> 10 5.000000e-01
#> 11 5.000000e-01
#> 12 5.000000e-01
#> 13 5.000000e-01
#> 14 5.000000e-01
#> 15 5.000000e-01
#> 16 5.000000e-01
#> 17 5.000000e-01
#> 18 5.000000e-01
#> 19 5.000000e-01
#> 20 5.000000e-01
#> 21 5.000000e-01
#> 22 5.000000e-01
#> 23 5.000000e-01
#> 24 5.000000e-01
#> 25 2.581802e-08
#> 26 2.581802e-08
#> 27 2.581802e-08
#> 28 1.751684e-09
#> 29 1.751684e-09
#> 30 1.751684e-09
#> siriusScore isotopeScore
#> 1 27.906019 1.966055
#> 2 27.906019 1.966055
#> 3 27.906019 1.966055
#> 4 27.906019 1.966055
#> 5 27.906019 1.966055
#> 6 27.906019 1.966055
#> 7 27.906019 1.966055
#> 8 27.906019 1.966055
#> 9 27.906019 1.966055
#> 10 27.906019 1.966055
#> 11 27.906019 1.966055
#> 12 27.906019 1.966055
#> 13 27.906019 1.966055
#> 14 27.906019 1.966055
#> 15 27.906019 1.966055
#> 16 27.906019 1.966055
#> 17 27.906019 1.966055
#> 18 27.906019 1.966055
#> 19 27.906019 1.966055
#> 20 27.906019 1.966055
#> 21 27.906019 1.966055
#> 22 27.906019 1.966055
#> 23 27.906019 1.966055
#> 24 27.906019 1.966055
#> 25 11.126973 0.000000
#> 26 11.126973 0.000000
#> 27 11.126973 0.000000
#> 28 8.436478 2.462666
#> 29 8.436478 2.462666
#> 30 8.436478 2.462666
#> treeScore xcms_fts
#> 1 25.939964 CP005
#> 2 25.939964 CP005
#> 3 25.939964 CP005
#> 4 25.939964 CP005
#> 5 25.939964 CP005
#> 6 25.939964 CP005
#> 7 25.939964 CP005
#> 8 25.939964 CP005
#> 9 25.939964 CP005
#> 10 25.939964 CP005
#> 11 25.939964 CP005
#> 12 25.939964 CP005
#> 13 25.939964 CP005
#> 14 25.939964 CP005
#> 15 25.939964 CP005
#> 16 25.939964 CP005
#> 17 25.939964 CP005
#> 18 25.939964 CP005
#> 19 25.939964 CP005
#> 20 25.939964 CP005
#> 21 25.939964 CP005
#> 22 25.939964 CP005
#> 23 25.939964 CP005
#> 24 25.939964 CP005
#> 25 11.126973 CP005
#> 26 11.126973 CP005
#> 27 11.126973 CP005
#> 28 5.973812 CP005
#> 29 5.973812 CP005
#> 30 5.973812 CP005
#> type fragmentId
#> 1 fragments 0
#> 2 fragments 1
#> 3 fragments 2
#> 4 fragments 3
#> 5 fragments 4
#> 6 fragments 5
#> 7 fragments 6
#> 8 losses NA
#> 9 losses NA
#> 10 losses NA
#> 11 losses NA
#> 12 losses NA
#> 13 losses NA
#> 14 fragments 0
#> 15 fragments 1
#> 16 fragments 2
#> 17 fragments 3
#> 18 fragments 4
#> 19 fragments 5
#> 20 losses NA
#> 21 losses NA
#> 22 losses NA
#> 23 losses NA
#> 24 losses NA
#> 25 fragments 0
#> 26 fragments 1
#> 27 losses NA
#> 28 fragments 0
#> 29 fragments 1
#> 30 losses NA
#> molecularFormula_fragment
#> 1 C4H9FN2O3
#> 2 C4H7FN2O2
#> 3 C3H8FNO2
#> 4 H6N2O2
#> 5 CH5FNO
#> 6 CO3
#> 7 CH5FO
#> 8 H2O
#> 9 CHNO
#> 10 C4HF
#> 11 C3H2NO
#> 12 C3H9FN2
#> 13 C3H2N2O
#> 14 C4H6FNO3
#> 15 C4H4FNO2
#> 16 C3H5FO2
#> 17 CO3
#> 18 H3NO2
#> 19 CH2FO
#> 20 H2O
#> 21 CHNO
#> 22 C3H6FN
#> 23 C4HF
#> 24 C3H2NO
#> 25 C7H14O
#> 26 C7H12
#> 27 H2O
#> 28 C7H8N2O2
#> 29 C6H7NO
#> 30 CHNO
#> adduct_fragment
#> 1 [M + H]+
#> 2 [M + H]+
#> 3 [M + H]+
#> 4 [M + H]+
#> 5 [M + H]+
#> 6 [M + H]+
#> 7 [M + H]+
#> 8 <NA>
#> 9 <NA>
#> 10 <NA>
#> 11 <NA>
#> 12 <NA>
#> 13 <NA>
#> 14 [M + H3N + H]+
#> 15 [M + H3N + H]+
#> 16 [M + H3N + H]+
#> 17 [M + H]+
#> 18 [M + H3N + H]+
#> 19 [M + H3N + H]+
#> 20 <NA>
#> 21 <NA>
#> 22 <NA>
#> 23 <NA>
#> 24 <NA>
#> 25 [M + K]+
#> 26 [M + K]+
#> 27 <NA>
#> 28 [M + H]+
#> 29 [M + H]+
#> 30 <NA>
#> massDeviationDa
#> 1 -1.094110e-03
#> 2 1.886956e-03
#> 3 -1.521303e-03
#> 4 3.332253e-04
#> 5 1.373113e-03
#> 6 -5.499752e-04
#> 7 1.631866e-03
#> 8 NA
#> 9 NA
#> 10 NA
#> 11 NA
#> 12 NA
#> 13 NA
#> 14 -1.094110e-03
#> 15 1.886956e-03
#> 16 -1.521303e-03
#> 17 -5.499752e-04
#> 18 3.332253e-04
#> 19 1.373113e-03
#> 20 NA
#> 21 NA
#> 22 NA
#> 23 NA
#> 24 NA
#> 25 -1.720458e-03
#> 26 1.260608e-03
#> 27 NA
#> 28 4.876187e-05
#> 29 -3.784309e-04
#> 30 NA
#> massDeviationPpm score
#> 1 -7.1479677 1.819346
#> 2 13.9714141 7.058971
#> 3 -13.8225289 4.258650
#> 4 4.9697631 4.758526
#> 5 20.4807207 6.926701
#> 6 -9.0172474 5.019691
#> 7 30.7659256 7.041774
#> 8 NA 6.849474
#> 9 NA 3.672010
#> 10 NA 2.902315
#> 11 NA 3.577534
#> 12 NA 3.314685
#> 13 NA 5.770656
#> 14 -7.1479677 1.819346
#> 15 13.9714141 12.829627
#> 16 -13.8225289 4.258650
#> 17 -9.0172474 5.019691
#> 18 4.9697631 4.758526
#> 19 20.4807207 6.926701
#> 20 NA 12.620130
#> 21 NA 3.672010
#> 22 NA 3.314685
#> 23 NA 2.902315
#> 24 NA 3.577534
#> 25 -11.2399829 3.557526
#> 26 9.3338027 7.778944
#> 27 NA 7.569447
#> 28 0.3185678 4.443024
#> 29 -3.4384156 4.580095
#> 30 NA 3.993454
#> intensity mz
#> 1 0.051592892 153.06590
#> 2 0.535645687 135.05832
#> 3 0.003872357 110.05966
#> 4 0.001187399 67.05054
#> 5 0.121864569 67.04417
#> 6 0.003774877 60.99147
#> 7 0.133356745 53.04135
#> 8 NA NA
#> 9 NA NA
#> 10 NA NA
#> 11 NA NA
#> 12 NA NA
#> 13 NA NA
#> 14 0.051592892 153.06590
#> 15 0.535645687 135.05832
#> 16 0.003872357 110.05966
#> 17 0.003774877 60.99147
#> 18 0.001187399 67.05054
#> 19 0.121864569 67.04417
#> 20 NA NA
#> 21 NA NA
#> 22 NA NA
#> 23 NA NA
#> 24 NA NA
#> 25 0.051592892 153.06590
#> 26 0.535645687 135.05832
#> 27 NA NA
#> 28 0.051592892 153.06590
#> 29 0.003872357 110.05966
#> 30 NA NA
#> sourceFragmentIdx
#> 1 NA
#> 2 NA
#> 3 NA
#> 4 NA
#> 5 NA
#> 6 NA
#> 7 NA
#> 8 0
#> 9 0
#> 10 1
#> 11 1
#> 12 0
#> 13 1
#> 14 NA
#> 15 NA
#> 16 NA
#> 17 NA
#> 18 NA
#> 19 NA
#> 20 0
#> 21 0
#> 22 0
#> 23 1
#> 24 1
#> 25 NA
#> 26 NA
#> 27 0
#> 28 NA
#> 29 NA
#> 30 0
#> targetFragmentIdx
#> 1 NA
#> 2 NA
#> 3 NA
#> 4 NA
#> 5 NA
#> 6 NA
#> 7 NA
#> 8 1
#> 9 2
#> 10 3
#> 11 4
#> 12 5
#> 13 6
#> 14 NA
#> 15 NA
#> 16 NA
#> 17 NA
#> 18 NA
#> 19 NA
#> 20 1
#> 21 2
#> 22 3
#> 23 4
#> 24 5
#> 25 NA
#> 26 NA
#> 27 1
#> 28 NA
#> 29 NA
#> 30 1Submit job to Sirius - For De Novo structure annotation.
De novo structure annotation is computationally intensive and recommended only for specific features.
# Determine features that do not have/have poor structure prediction
fts_denovo <-summarytb$alignedFeatureId[which(
summarytb$confidenceApproxMatch < 0.3 |
summarytb$confidenceApproxMatch %in% c("NA", "-Infinity"))]
# Compute with zodiac and denovo
job_id <- run(srs,
msNovelistParams = deNovoStructureParam(numberOfCandidateToPredict = 5),
alignedFeaturesIds = fts_denovo,
recompute = FALSE,
wait = TRUE
)
## Get info for the job
jobInfo(srs, job_id) |> cat()
#> Job ID: 2
#>
#> Command:
#> --FormulaSettings.fallback=S
#> --FormulaSearchSettings.applyFormulaConstraintsToBottomUp=false
#> --IsotopeSettings.filter=true
#> --UseHeuristic.useOnlyHeuristicAboveMz=650
#> --InjectSpectralLibraryMatchFormulas.minScoreToInject=0.7
#> --FormulaSearchDB=
#> --InjectSpectralLibraryMatchFormulas.minPeakMatchesToInject=6
#> --FormulaSettings.enforced=HCNOP
#> --InjectSpectralLibraryMatchFormulas.injectFormulas=true
#> --AdductSettings.detectable=[M+H3N+H]+,[M-H4O2+H]+,[M-H2O-H]-,[M-H3N-H]-,[M+Cl]-,[2M+K]+,[M+K]+,[2M+Cl]-,[M+C2H4O2-H]-,[M+H]+,[2M+H]+,[M-CH3-H]-,[M-H]-,[M+Na]+,[M-H2O+H]+
#> --RecomputeResults=false
#> --FormulaResultThreshold=true
#> --InjectSpectralLibraryMatchFormulas.alwaysPredict=false
#> --UseHeuristic.useHeuristicAboveMz=300
#> --IsotopeMs2Settings=IGNORE
#> --MS2MassDeviation.allowedMassDeviation=10.0ppm
#> --FormulaSearchSettings.applyFormulaConstraintsToDatabaseCandidates=false
#> --EnforceElGordoFormula=true
#> --NumberOfCandidatesPerIonization=1
#> --FormulaSettings.detectable=B,S,Cl,Se,Br
#> --AdductSettings.fallback=[M+H]+,[M-H]-,[M+Na]+,[M+K]+
#> --NumberOfCandidates=10
#> --FormulaSearchSettings.performBottomUpAboveMz=0.0
#> --NumberOfMsNovelistCandidates=5
#> formulas
#> fingerprints
#> classes
#> denovo-structures
#>
#> Progress:
#> State: DONE
#> Current Progress: 57100
#> Max Progress: 57100
#>
#> Affected Compound IDs:
#> 819205328450128305, 819205328450128304, 819205328450128303, 819205328450128302, 819205328450128301, 819205328450128300, 819205328450128299, 819205328450128298, 819205328450128297, 819205328450128296, 819205328450128295, 819205328450128294, 819205328450128293, 819205328450128292, 819205328450128291, 819205328450128290, 819205328450128289, 819205328450128288, 819205328445933983, 819205328445933982, 819205328445933981, 819205328445933980, 819205328445933979, 819205328445933978, 819205328445933977, 819205328445933976, 819205328445933975, 819205328445933974, 819205328445933973, 819205328445933972, 819205328445933971, 819205328445933970, 819205328445933969, 819205328445933968, 819205328445933967, 819205328445933966, 819205328445933965, 819205328445933964, 819205328445933963, 819205328445933962, 819205328445933961, 819205328445933960, 819205328445933959, 819205328445933958, 819205328445933957, 819205328445933956, 819205328445933955, 819205328445933954, 819205328445933953, 819205328445933952, 819205328445933951, 819205328445933950, 819205328445933949, 819205328445933948, 819205328445933947, 819205328445933946, 819205328445933945, 819205328445933944, 819205328445933943, 819205328445933942, 819205328445933941, 819205328445933940, 819205328445933939, 819205328445933938, 819205328445933937, 819205328445933936, 819205328445933935, 819205328445933934, 819205328445933933, 819205328445933932, 819205328445933931, 819205328445933930, 819205328445933929, 819205328445933928, 819205328445933927, 819205328445933926, 819205328445933925, 819205328445933924, 819205328445933923, 819205328445933922, 819205328445933921, 819205328445933920, 819205328445933919, 819205328445933918, 819205328445933917, 819205328445933916, 819205328445933915, 819205328445933914, 819205328445933913, 819205328445933912, 819205328445933911, 819205328445933910, 819205328445933909, 819205328445933908, 819205328445933907, 819205328445933906, 819205328445933905, 819205328445933904, 819205328445933903, 819205328445933902, 819205328445933901, 819205328445933900, 819205328445933899, 819205328445933898, 819205328445933897, 819205328445933896, 819205328445933895, 819205328445933894, 819205328445933893, 819205328445933892, 819205328445933891, 819205328445933890, 819205328445933889, 819205328445933888
#>
#> Affected Aligned Feature IDs:
#> 819205329515481635
#> 819205329511287330
#> 819205329511287329
#> 819205329502898720
#> 819205329502898719
#> 819205329502898718
#> 819205329502898717
#> 819205329498704412
#> 819205329498704411
#> 819205329498704410
#> 819205329498704409
#> 819205329494510104
#> 819205329494510103
#> 819205329490315798
#> 819205329486121493
#> 819205329486121492
#> 819205329481927187
#> 819205329481927186
#> 819205329477732881
#> 819205329473538576
#> 819205329469344271
#> 819205329465149966
#> 819205329465149965
#> 819205329456761356
#> 819205329456761355
#> 819205329452567050
#> 819205329448372745
#> 819205329448372744
#> 819205329444178439
#> 819205329444178438
#> 819205329439984133
#> 819205329439984132
#> 819205329435789827
#> 819205329435789826
#> 819205329431595521
#> 819205329427401216
#> 819205329427401215
#> 819205329423206910
#> 819205329423206909
#> 819205329419012604
#> 819205329414818299
#> 819205329414818298
#> 819205329410623993
#> 819205329406429688
#> 819205329402235383
#> 819205329393846774
#> 819205329393846773
#> 819205329389652468
#> 819205329385458163
#> 819205329381263858
#> 819205329372875249
#> 819205329372875248
#> 819205329368680943
#> 819205329326737902
#> 819205329322543597
#> 819205329318349292
#> 819205329301572075
#> 819205329297377770
#> 819205329293183465
#> 819205329259629032
#> 819205329255434727
#> 819205329251240422
#> 819205329247046117
#> 819205329242851812
#> 819205329242851811
#> 819205329238657506
#> 819205329234463201
#> 819205329230268896
#> 819205329230268895
#> 819205329226074590
#> 819205329213491677
#> 819205329209297372
#> 819205329200908763
#> 819205329179937242
#> 819205329179937241
#> 819205329175742936
#> 819205329175742935
#> 819205329171548630
#> 819205329167354325
#> 819205329163160020
#> 819205329117022675
#> 819205329112828370
#> 819205329108634065
#> 819205329108634064
#> 819205329096051151
#> 819205329096051150
#> 819205329096051149
#> 819205329091856844
#> 819205329087662539
#> 819205329079273930
#> 819205329075079625
#> 819205329066691016
#> 819205329058302407
#> 819205329054108102
#> 819205329041525189
#> 819205329028942276
#> 819205329012165059
#> 819205328995387842
#> 819205328982804929
#> 819205328970222016
#> 819205328932473279
#> 819205328919890366
#> 819205328903113149
#> 819205328886335932
#> 819205328869558715
#> 819205328861170106
#> 819205328844392889
#> 819205328831809976
#> 819205328810838455
#> 819205328798255542
#> 819205328781478325
#> 819205328735340980
#> 819205328718563763
#> 819205328622094770Retrieve results
summraryDeNovo <- summary(srs, result.type = "deNovo")
head(summraryDeNovo)
#> alignedFeatureId
#> 1 819205328622094770
#> 2 819205328718563763
#> 3 819205328735340980
#> 4 819205328781478325
#> 5 819205328798255542
#> 6 819205328810838455
#> compoundId
#> 1 819205328445933888
#> 2 819205328445933889
#> 3 819205328445933890
#> 4 819205328445933891
#> 5 819205328445933892
#> 6 819205328445933893
#> externalFeatureId ionMass
#> 1 CP001 0.0000
#> 2 CP002 0.0000
#> 3 CP003 220.0975
#> 4 CP004 219.0932
#> 5 CP005 153.0656
#> 6 CP006 235.1442
#> charge hasMs1 hasMsMs
#> 1 1 TRUE FALSE
#> 2 1 TRUE FALSE
#> 3 1 TRUE TRUE
#> 4 1 TRUE TRUE
#> 5 1 TRUE TRUE
#> 6 1 TRUE TRUE
#> formulaId
#> 1 819205523682397402
#> 2 819205528308714745
#> 3 819205520754773184
#> 4 819205514274573431
#> 5 819205517835537576
#> 6 819205510843632741
#> molecularFormula adduct
#> 1 C6H12N6O3 [M + H]+
#> 2 C10H16O5 [M + H]+
#> 3 C10H10FN5 [M + H]+
#> 4 C12H14N2S [M + H]+
#> 5 C4H9FN2O3 [M + H]+
#> 6 C10H19FN2O3 [M + H]+
#> rank siriusScoreNormalized
#> 1 1 0.08222814
#> 2 1 0.07231049
#> 3 2 0.09484521
#> 4 1 0.94680986
#> 5 1 0.49999999
#> 6 1 0.99585317
#> siriusScore isotopeScore
#> 1 0.000000 0.000000
#> 2 0.000000 0.000000
#> 3 6.372408 0.000000
#> 4 48.071033 0.000000
#> 5 27.906019 1.966055
#> 6 27.272863 4.595855
#> treeScore formulaId.1
#> 1 0.000000 819205523682397402
#> 2 0.000000 819205528308714745
#> 3 6.372408 819205520754773184
#> 4 48.071033 819205514274573431
#> 5 25.939964 819205517835537576
#> 6 22.677008 819205510843632741
#> molecularFormula.1 adduct.1
#> 1 C6H12N6O3 [M + H]+
#> 2 C10H16O5 [M + H]+
#> 3 C10H10FN5 [M + H]+
#> 4 C12H14N2S [M + H]+
#> 5 C4H9FN2O3 [M + H]+
#> 6 C10H19FN2O3 [M + H]+
#> rank.1
#> 1 1
#> 2 1
#> 3 1
#> 4 1
#> 5 1
#> 6 1
#> siriusScoreNormalized.1
#> 1 0.08222814
#> 2 0.07231049
#> 3 0.09484521
#> 4 0.94680986
#> 5 0.49999999
#> 6 0.99585317
#> siriusScore.1 isotopeScore.1
#> 1 0.000000 0.000000
#> 2 0.000000 0.000000
#> 3 6.372408 0.000000
#> 4 48.071033 0.000000
#> 5 27.906019 1.966055
#> 6 27.272863 4.595855
#> treeScore.1 computing
#> 1 0.000000 FALSE
#> 2 0.000000 FALSE
#> 3 6.372408 FALSE
#> 4 48.071033 FALSE
#> 5 25.939964 FALSE
#> 6 22.677008 FALSE
#> inchiKey
#> 1 <NA>
#> 2 <NA>
#> 3 JZOXOBXBBIFYSC
#> 4 UUVNICFMINSQCH
#> 5 OKHHVSOXIKKYPM
#> 6 FLEAFHNQGJZFAF
#> smiles
#> 1 <NA>
#> 2 <NA>
#> 3 Cc1ccc(Nc2ncnc(N)n2)cc1F
#> 4 Cc1csc(Nc2c(C)cccc2C)n1
#> 5 O=C(F)NCNCCOO
#> 6 O=C(NC1CCCCC1)NC(O)(O)CCF
#> xlogP csiScore
#> 1 NA NA
#> 2 NA NA
#> 3 0 -90.94557
#> 4 0 -53.58922
#> 5 0 -102.35347
#> 6 0 -155.98293
#> tanimotoSimilarity type
#> 1 NA <NA>
#> 2 NA <NA>
#> 3 0.5194805 NPC
#> 4 0.6447368 NPC
#> 5 0.3205128 NPC
#> 6 0.7200000 NPC
#> level levelIndex
#> 1 <NA> NA
#> 2 <NA> NA
#> 3 PATHWAY 0
#> 4 PATHWAY 0
#> 5 PATHWAY 0
#> 6 PATHWAY 0
#> name
#> 1 <NA>
#> 2 <NA>
#> 3 Alkaloids
#> 4 Alkaloids
#> 5 Amino acids and Peptides
#> 6 Alkaloids
#> description
#> 1 <NA>
#> 2 <NA>
#> 3 Pathway: Alkaloids
#> 4 Pathway: Alkaloids
#> 5 Pathway: Amino acids and Peptides
#> 6 Pathway: Alkaloids
#> id probability index type.1
#> 1 NA NA NA <NA>
#> 2 NA NA NA <NA>
#> 3 0 0.8597484 0 NPC
#> 4 0 0.6377908 0 NPC
#> 5 1 0.1932061 1 NPC
#> 6 0 0.2922554 0 NPC
#> level.1 levelIndex.1
#> 1 <NA> NA
#> 2 <NA> NA
#> 3 SUPERCLASS 1
#> 4 SUPERCLASS 1
#> 5 SUPERCLASS 1
#> 6 SUPERCLASS 1
#> name.1
#> 1 <NA>
#> 2 <NA>
#> 3 Pseudoalkaloids (transamidation)
#> 4 Tryptophan alkaloids
#> 5 Small peptides
#> 6 Pseudoalkaloids (transamidation)
#> description.1
#> 1 <NA>
#> 2 <NA>
#> 3 Superclass: Pseudoalkaloids (transamidation)
#> 4 Superclass: Tryptophan alkaloids
#> 5 Superclass: Small peptides
#> 6 Superclass: Pseudoalkaloids (transamidation)
#> id.1 probability.1 index.1
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 59 0.14546104 59
#> 4 72 0.08722231 72
#> 5 63 0.28825998 63
#> 6 59 0.32983977 59
#> type.2 level.2 levelIndex.2
#> 1 <NA> <NA> NA
#> 2 <NA> <NA> NA
#> 3 NPC CLASS 2
#> 4 NPC CLASS 2
#> 5 NPC CLASS 2
#> 6 NPC CLASS 2
#> name.2
#> 1 <NA>
#> 2 <NA>
#> 3 Purine alkaloids
#> 4 Pyridine alkaloids
#> 5 Aminoacids
#> 6 Purine alkaloids
#> description.2
#> 1 <NA>
#> 2 <NA>
#> 3 Class: Purine alkaloids
#> 4 Class: Pyridine alkaloids
#> 5 Class: Aminoacids
#> 6 Class: Purine alkaloids
#> id.2 probability.2 index.2
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 597 0.06170827 597
#> 4 602 0.05239901 602
#> 5 109 0.42593104 109
#> 6 597 0.13299610 597
#> rank.2 inchiKey.1
#> 1 NA <NA>
#> 2 NA <NA>
#> 3 2 JZOXOBXBBIFYSC
#> 4 1 UUVNICFMINSQCH
#> 5 1 OKHHVSOXIKKYPM
#> 6 1 FLEAFHNQGJZFAF
#> smiles.1
#> 1 <NA>
#> 2 <NA>
#> 3 Cc1ccc(Nc2ncnc(N)n2)cc1F
#> 4 Cc1csc(Nc2c(C)cccc2C)n1
#> 5 O=C(F)NCNCCOO
#> 6 O=C(NC1CCCCC1)NC(O)(O)CCF
#> xlogP.1 rank.3 csiScore.1
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 0 1 -90.94557
#> 4 0 1 -53.58922
#> 5 0 1 -102.35347
#> 6 0 1 -155.98293
#> tanimotoSimilarity.1 type.3
#> 1 NA <NA>
#> 2 NA <NA>
#> 3 0.5194805 NPC
#> 4 0.6447368 NPC
#> 5 0.3205128 NPC
#> 6 0.7200000 NPC
#> level.3 levelIndex.3
#> 1 <NA> NA
#> 2 <NA> NA
#> 3 PATHWAY 0
#> 4 PATHWAY 0
#> 5 PATHWAY 0
#> 6 PATHWAY 0
#> name.3
#> 1 <NA>
#> 2 <NA>
#> 3 Alkaloids
#> 4 Alkaloids
#> 5 Amino acids and Peptides
#> 6 Alkaloids
#> description.3
#> 1 <NA>
#> 2 <NA>
#> 3 Pathway: Alkaloids
#> 4 Pathway: Alkaloids
#> 5 Pathway: Amino acids and Peptides
#> 6 Pathway: Alkaloids
#> id.3 probability.3 index.3
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 0 0.8597484 0
#> 4 0 0.6377908 0
#> 5 1 0.1932061 1
#> 6 0 0.2922554 0
#> type.4 level.4
#> 1 <NA> <NA>
#> 2 <NA> <NA>
#> 3 NPC SUPERCLASS
#> 4 NPC SUPERCLASS
#> 5 NPC SUPERCLASS
#> 6 NPC SUPERCLASS
#> levelIndex.4
#> 1 NA
#> 2 NA
#> 3 1
#> 4 1
#> 5 1
#> 6 1
#> name.4
#> 1 <NA>
#> 2 <NA>
#> 3 Pseudoalkaloids (transamidation)
#> 4 Tryptophan alkaloids
#> 5 Small peptides
#> 6 Pseudoalkaloids (transamidation)
#> description.4
#> 1 <NA>
#> 2 <NA>
#> 3 Superclass: Pseudoalkaloids (transamidation)
#> 4 Superclass: Tryptophan alkaloids
#> 5 Superclass: Small peptides
#> 6 Superclass: Pseudoalkaloids (transamidation)
#> id.4 probability.4 index.4
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 59 0.14546104 59
#> 4 72 0.08722231 72
#> 5 63 0.28825998 63
#> 6 59 0.32983977 59
#> type.5 level.5 levelIndex.5
#> 1 <NA> <NA> NA
#> 2 <NA> <NA> NA
#> 3 NPC CLASS 2
#> 4 NPC CLASS 2
#> 5 NPC CLASS 2
#> 6 NPC CLASS 2
#> name.5
#> 1 <NA>
#> 2 <NA>
#> 3 Purine alkaloids
#> 4 Pyridine alkaloids
#> 5 Aminoacids
#> 6 Purine alkaloids
#> description.5
#> 1 <NA>
#> 2 <NA>
#> 3 Class: Purine alkaloids
#> 4 Class: Pyridine alkaloids
#> 5 Class: Aminoacids
#> 6 Class: Purine alkaloids
#> id.5 probability.5 index.5
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 597 0.06170827 597
#> 4 602 0.05239901 602
#> 5 109 0.42593104 109
#> 6 597 0.13299610 597
#> structureName
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> structureName.1
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>Below is the full results.
full_de_novo <- results(srs,
return.type = "data.frame",
result.type = "deNovo",
topFormula = 5)
head(full_de_novo)
#> formulaId
#> 1 819205523682397402
#> 2 819205523682397403
#> 3 819205523682397404
#> 4 819205523682397405
#> 5 819205523682397406
#> 6 819205528308714745
#> molecularFormula adduct
#> 1 C6H12N6O3 [M + H]+
#> 2 C8H15F3O3 [M + H]+
#> 3 C8H18O5 [M + Na]+
#> 4 C9H14N4O [M + Na]+
#> 5 C6H18N4O2 [M + K]+
#> 6 C10H16O5 [M + H]+
#> rank siriusScoreNormalized
#> 1 1 0.08222814
#> 2 2 0.08222814
#> 3 3 0.08222814
#> 4 4 0.08222814
#> 5 5 0.08222814
#> 6 1 0.07231049
#> siriusScore isotopeScore
#> 1 0 0
#> 2 0 0
#> 3 0 0
#> 4 0 0
#> 5 0 0
#> 6 0 0
#> treeScore xcms_fts
#> 1 0 CP001
#> 2 0 CP001
#> 3 0 CP001
#> 4 0 CP001
#> 5 0 CP001
#> 6 0 CP002
#> sirius_fts rank.x
#> 1 819205328622094770 NA
#> 2 819205328622094770 NA
#> 3 819205328622094770 NA
#> 4 819205328622094770 NA
#> 5 819205328622094770 NA
#> 6 819205328718563763 NA
#> inchiKey smiles xlogP rank.y
#> 1 <NA> <NA> NA NA
#> 2 <NA> <NA> NA NA
#> 3 <NA> <NA> NA NA
#> 4 <NA> <NA> NA NA
#> 5 <NA> <NA> NA NA
#> 6 <NA> <NA> NA NA
#> csiScore tanimotoSimilarity
#> 1 NA NA
#> 2 NA NA
#> 3 NA NA
#> 4 NA NA
#> 5 NA NA
#> 6 NA NA
#> structureName
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>Setting a Known Molecular Formula
When you already know (or suspect) the molecular formula and adduct for a feature, you can restrict Sirius formula identification to that candidate. This is useful for targeted analyses where you want to compute the fragmentation tree for a known compound rather than performing an open search.
Use the candidateFormulas parameter of
formulaIdParam() together with enforceAdducts
to lock in both the formula and adduct:
# Select a feature with MS2 data (e.g. Carbaryl, [M+H]+ at m/z ~220.10)
fi <- featuresInfo(srs)
target_ft <- fi[fi[, "hasMsMs"] == TRUE, "alignedFeatureId"][[1]]
# Run formula identification restricted to a single known formula
job_id <- run(srs,
alignedFeaturesIds = target_ft,
enforceAdducts = "[M+H]+",
formulaIdParams = formulaIdParam(
candidateFormulas = "C12H13NO3"
),
recompute = TRUE,
wait = TRUE)You can also supply multiple candidate formulas if you want to compare a small set of possibilities:
job_id <- run(srs,
alignedFeaturesIds = target_ft,
enforceAdducts = "[M+H]+",
formulaIdParams = formulaIdParam(
candidateFormulas = c("C12H13NO3", "C10H12N2O")
),
recompute = TRUE,
wait = TRUE)After the job completes, retrieve the formula results and fragmentation tree as usual:
# Formula results - should only contain the specified candidate(s)
results(srs,
features = target_ft,
result.type = "formulaId",
return.type = "data.frame")
#> formulaId
#> 1 819207515184100003
#> molecularFormula adduct
#> 1 C12H13NO3 [M + H]+
#> rank siriusScoreNormalized
#> 1 1 1
#> siriusScore isotopeScore
#> 1 7.239287 0
#> treeScore xcms_fts
#> 1 7.239287 CP003
#> sirius_fts
#> 1 819205328735340980
# Fragmentation tree for the known formula
results(srs,
features = target_ft,
result.type = "fragTree",
topFormula = 1,
return.type = "list")
#> $`819205328735340980`
#> formulaId
#> 1 819207515184100003
#> 2 819207515184100003
#> 3 819207515184100003
#> molecularFormula adduct
#> 1 C12H13NO3 [M + H]+
#> 2 C12H13NO3 [M + H]+
#> 3 C12H13NO3 [M + H]+
#> rank siriusScoreNormalized
#> 1 1 1
#> 2 1 1
#> 3 1 1
#> siriusScore isotopeScore
#> 1 7.239287 0
#> 2 7.239287 0
#> 3 7.239287 0
#> treeScore xcms_fts type
#> 1 7.239287 CP003 fragments
#> 2 7.239287 CP003 fragments
#> 3 7.239287 CP003 losses
#> fragmentId
#> 1 0
#> 2 1
#> 3 NA
#> molecularFormula_fragment
#> 1 C12H13NO3
#> 2 C10H9N
#> 3 C2H4O3
#> adduct_fragment
#> 1 [M + H]+
#> 2 [M + H]+
#> 3 <NA>
#> massDeviationDa
#> 1 9.891098e-04
#> 2 9.584194e-05
#> 3 NA
#> massDeviationPpm score
#> 1 4.4939557 1.574046
#> 2 0.6651955 7.158566
#> 3 NA 5.665241
#> intensity mz
#> 1 1.00000000 220.0978
#> 2 0.06788801 144.0809
#> 3 NA NA
#> sourceFragmentIdx
#> 1 NA
#> 2 NA
#> 3 0
#> targetFragmentIdx
#> 1 NA
#> 2 NA
#> 3 1CleanUp
# Close the Sirius session
shutdown(srs)
#> Sirius was shut down successfullySession information
The R code was run on:
date()
#> [1] "Tue Mar 10 14:58:15 2026"Information on the R session:
sessionInfo()
#> R version 4.5.2 (2025-10-31 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 26200)
#>
#> Matrix products: default
#> LAPACK version 3.12.1
#>
#> locale:
#> [1] LC_COLLATE=English_United Kingdom.utf8
#> [2] LC_CTYPE=English_United Kingdom.utf8
#> [3] LC_MONETARY=English_United Kingdom.utf8
#> [4] LC_NUMERIC=C
#> [5] LC_TIME=English_United Kingdom.utf8
#>
#> time zone: Europe/Paris
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats4 stats
#> [3] graphics grDevices
#> [5] utils datasets
#> [7] methods base
#>
#> other attached packages:
#> [1] MsDataHub_1.10.0
#> [2] dplyr_1.2.0
#> [3] RuSirius_0.2.5
#> [4] jsonlite_2.0.0
#> [5] MetaboAnnotation_1.14.0
#> [6] RSirius_6.3.3
#> [7] xcms_4.8.0
#> [8] MsExperiment_1.12.0
#> [9] ProtGenerics_1.42.0
#> [10] Spectra_1.20.1
#> [11] BiocParallel_1.44.0
#> [12] S4Vectors_0.48.0
#> [13] BiocGenerics_0.56.0
#> [14] generics_0.1.4
#>
#> loaded via a namespace (and not attached):
#> [1] RColorBrewer_1.1-3
#> [2] MultiAssayExperiment_1.36.1
#> [3] magrittr_2.0.4
#> [4] farver_2.1.2
#> [5] MALDIquant_1.22.3
#> [6] fs_1.6.6
#> [7] vctrs_0.7.1
#> [8] memoise_2.0.1
#> [9] RCurl_1.98-1.17
#> [10] base64enc_0.1-6
#> [11] htmltools_0.5.9
#> [12] S4Arrays_1.10.1
#> [13] BiocBaseUtils_1.12.0
#> [14] progress_1.2.3
#> [15] curl_7.0.0
#> [16] AnnotationHub_4.0.0
#> [17] SparseArray_1.10.8
#> [18] mzID_1.48.0
#> [19] htmlwidgets_1.6.4
#> [20] plyr_1.8.9
#> [21] httr2_1.2.2
#> [22] impute_1.84.0
#> [23] cachem_1.1.0
#> [24] igraph_2.2.2
#> [25] lifecycle_1.0.5
#> [26] iterators_1.0.14
#> [27] pkgconfig_2.0.3
#> [28] Matrix_1.7-4
#> [29] R6_2.6.1
#> [30] fastmap_1.2.0
#> [31] MatrixGenerics_1.22.0
#> [32] clue_0.3-67
#> [33] digest_0.6.39
#> [34] pcaMethods_2.2.0
#> [35] rsvg_2.7.0
#> [36] ps_1.9.1
#> [37] AnnotationDbi_1.72.0
#> [38] ExperimentHub_3.0.0
#> [39] GenomicRanges_1.62.1
#> [40] RSQLite_2.4.6
#> [41] filelock_1.0.3
#> [42] httr_1.4.8
#> [43] abind_1.4-8
#> [44] compiler_4.5.2
#> [45] withr_3.0.2
#> [46] bit64_4.6.0-1
#> [47] doParallel_1.0.17
#> [48] S7_0.2.1
#> [49] DBI_1.2.3
#> [50] MASS_7.3-65
#> [51] ChemmineR_3.62.0
#> [52] rappdirs_0.3.4
#> [53] DelayedArray_0.36.0
#> [54] rjson_0.2.23
#> [55] mzR_2.44.0
#> [56] tools_4.5.2
#> [57] PSMatch_1.14.0
#> [58] otel_0.2.0
#> [59] CompoundDb_1.14.2
#> [60] glue_1.8.0
#> [61] QFeatures_1.20.0
#> [62] grid_4.5.2
#> [63] cluster_2.1.8.1
#> [64] reshape2_1.4.5
#> [65] snow_0.4-4
#> [66] gtable_0.3.6
#> [67] preprocessCore_1.72.0
#> [68] tidyr_1.3.2
#> [69] data.table_1.18.2.1
#> [70] hms_1.1.4
#> [71] MetaboCoreUtils_1.19.2
#> [72] xml2_1.5.2
#> [73] XVector_0.50.0
#> [74] BiocVersion_3.22.0
#> [75] foreach_1.5.2
#> [76] pillar_1.11.1
#> [77] stringr_1.6.0
#> [78] limma_3.66.0
#> [79] BiocFileCache_3.0.0
#> [80] lattice_0.22-7
#> [81] bit_4.6.0
#> [82] tidyselect_1.2.1
#> [83] Biostrings_2.78.0
#> [84] knitr_1.51
#> [85] gridExtra_2.3
#> [86] IRanges_2.44.0
#> [87] Seqinfo_1.0.0
#> [88] SummarizedExperiment_1.40.0
#> [89] xfun_0.56
#> [90] Biobase_2.70.0
#> [91] statmod_1.5.1
#> [92] MSnbase_2.36.0
#> [93] matrixStats_1.5.0
#> [94] DT_0.34.0
#> [95] stringi_1.8.7
#> [96] yaml_2.3.12
#> [97] lazyeval_0.2.2
#> [98] evaluate_1.0.5
#> [99] codetools_0.2-20
#> [100] MsCoreUtils_1.22.1
#> [101] tibble_3.3.1
#> [102] BiocManager_1.30.27
#> [103] cli_3.6.5
#> [104] affyio_1.80.0
#> [105] processx_3.8.6
#> [106] Rcpp_1.1.1
#> [107] MassSpecWavelet_1.76.0
#> [108] dbplyr_2.5.2
#> [109] png_0.1-8
#> [110] XML_3.99-0.22
#> [111] parallel_4.5.2
#> [112] ggplot2_4.0.2
#> [113] blob_1.3.0
#> [114] prettyunits_1.2.0
#> [115] AnnotationFilter_1.34.0
#> [116] bitops_1.0-9
#> [117] MsFeatures_1.18.0
#> [118] scales_1.4.0
#> [119] affy_1.88.0
#> [120] ncdf4_1.24
#> [121] purrr_1.2.1
#> [122] crayon_1.5.3
#> [123] rlang_1.1.7
#> [124] KEGGREST_1.50.0
#> [125] vsn_3.78.1