MS backend accessing the MassBank MySQL database — MsBackendMassbankSql • MsBackendMassbank

The MsBackendMassbankSql provides access to mass spectrometry data from MassBank by directly accessing its MySQL/MariaDb database. In addition it supports adding new spectra variables or locally changing spectra variables provided by MassBank (without changing the original values in the database).

Note that MsBackendMassbankSql requires a local installation of the MassBank database since direct database access is not supported for the main MassBank instance.

Also, some of the fields in the MassBank database are not directly compatible with Spectra, such as the collision energy which is not available as a numeric value. The collision energy as available in MassBank is reported as spectra variable "collision_energy_text". Also, precursor m/z values reported for some spectra can not be converted to a numeric and hence NA is reported with the spectra variable precursorMz for these spectra. The variable "precursor_mz_text" can be used to get the original precursor m/z reported in MassBank.

Finally, MsBackendMassbankSql does not support parallel processing because the database connection stored within the object can not be shared acrcoss parallel processes. All functions on Spectra objects with a MsBackendMassbankSql will (silently) disable parallel processing even if the user provides a dedicated parallel processing setup with the BPPARAM parameter.

Usage

MsBackendMassbankSql()

# S4 method for class 'MsBackendMassbankSql'
backendInitialize(object, dbcon, ...)

# S4 method for class 'MsBackendMassbankSql'
peaksData(object, columns = peaksVariables(object))

# S4 method for class 'MsBackendMassbankSql'
dataStorage(object)

# S4 method for class 'MsBackendMassbankSql'
intensity(object) <- value

# S4 method for class 'MsBackendMassbankSql'
mz(object) <- value

# S4 method for class 'MsBackendMassbankSql'
reset(object)

# S4 method for class 'MsBackendMassbankSql'
spectraData(object, columns = spectraVariables(object))

# S4 method for class 'MsBackendMassbankSql'
spectraNames(object)

# S4 method for class 'MsBackendMassbankSql'
spectraNames(object) <- value

# S4 method for class 'MsBackendMassbankSql'
tic(object, initial = TRUE)

# S4 method for class 'MsBackendMassbankSql'
x[i, j, ..., drop = FALSE]

# S4 method for class 'MsBackendMassbankSql,ANY'
extractByIndex(object, i)

# S4 method for class 'Spectra'
compounds(object, ...)

# S4 method for class 'MsBackendMassbankSql'
compounds(object, ...)

# S4 method for class 'MsBackendMassbankSql'
x$name <- value

# S4 method for class 'MsBackendMassbankSql'
precScanNum(object)

# S4 method for class 'MsBackendMassbankSql'
backendBpparam(object, BPPARAM = bpparam())

Arguments

object: Object extending MsBackendMassbankSql.
dbcon: For backendInitialize,MsBackendMassbankSql: SQL database connection to the MassBank (MariaDb) database.
...: Additional arguments.
columns: For spectraData accessor: optional character with column names (spectra variables) that should be included in the returned DataFrame. By default, all columns are returned. For peaksData accessor: optional character with requested columns in the individual matrix of the returned list. Use peaksVariables(object) for supported columns.
value: replacement value for <- methods. See individual method description or expected data type.
initial: For tic: logical(1) whether the initially reported total ion current should be reported, or whether the total ion current should be (re)calculated on the actual data (initial = FALSE).
x: Object extending MsBackendMassbankSql.
i: For [: integer, logical or character to subset the object.
j: For [: not supported.
drop: For [: not considered.
name: name of the variable to replace for <- methods. See individual method description or expected data type.
BPPARAM: for backendBpparam: BiocParallel parallel processing setup. See BiocParallel::bpparam() for more information.
spectraVariables: For selectSpectraVariables: character with the names of the spectra variables to which the backend should be subsetted.

Value

See documentation of respective function.

Supported Backend functions

The following functions are supported by the MsBackendMassbankSql.

[: subset the backend. Only subsetting by element (row/i) is allowed
$, $<-: access or set/add a single spectrum variable (column) in the backend.
acquisitionNum: returns the acquisition number of each spectrum. Returns an integer of length equal to the number of spectra (with NA_integer_ if not available).
peaksData returns a list with the spectras' peak data. The length of the list is equal to the number of spectra in object. Each element of the list is a matrix with columns "mz" and "intensity". For an empty spectrum, a matrix with 0 rows and two columns (named mz and intensity) is returned. Parameter columns allows to select which peaks variables to return, but supports currently only "mz" and "intensity".
backendBpparam: whether the backend supports parallel processing. Takes a MsBackendMassbankSql and a parallel processing setup (see BiocParallel::bpparam() for details) as input and always returns a BiocParallel::SerialParam(). This function can be used to test whether a provided parallel processing setup is supported by the backend and returns the supported setup.
backendInitialize: initialises the backend by retrieving the IDs of all spectra in the database. Parameter dbcon with the connection to the MassBank MySQL database is required.
dataOrigin: gets a character of length equal to the number of spectra in object with the data origin of each spectrum. This could e.g. be the mzML file from which the data was read.
dataStorage: returns "<MassBank>" for all spectra.
centroided, centroided<-: gets or sets the centroiding information of the spectra. centroided returns a logical vector of length equal to the number of spectra with TRUE if a spectrum is centroided, FALSE if it is in profile mode and NA if it is undefined. See also isCentroided for estimating from the spectrum data whether the spectrum is centroided. value for centroided<- is either a single logical or a logical of length equal to the number of spectra in object.
collisionEnergy, collisionEnergy<-: gets or sets the collision energy for all spectra in object. collisionEnergy returns a numeric with length equal to the number of spectra (NA_real_ if not present/defined), collisionEnergy<- takes a numeric of length equal to the number of spectra in object. Note that the collision energy description from MassBank are provided as spectra variable "collisionEnergyText".
intensity: gets the intensity values from the spectra. Returns a IRanges::NumericList() of numeric vectors (intensity values for each spectrum). The length of the list is equal to the number of spectra in object.
ionCount: returns a numeric with the sum of intensities for each spectrum. If the spectrum is empty (see isEmpty), NA_real_ is returned.
isCentroided: a heuristic approach assessing if the spectra in object are in profile or centroided mode. The function takes the qtl th quantile top peaks, then calculates the difference between adjacent m/z value and returns TRUE if the first quartile is greater than k. (See Spectra:::.isCentroided for the code.)
isEmpty: checks whether a spectrum in object is empty (i.e. does not contain any peaks). Returns a logical vector of length equal number of spectra.
isolationWindowLowerMz, isolationWindowLowerMz<-: gets or sets the lower m/z boundary of the isolation window.
isolationWindowTargetMz, isolationWindowTargetMz<-: gets or sets the target m/z of the isolation window.
isolationWindowUpperMz, isolationWindowUpperMz<-: gets or sets the upper m/z boundary of the isolation window.
isReadOnly: returns a logical(1) whether the backend is read only or does allow also to write/update data.
length: returns the number of spectra in the object.
lengths: gets the number of peaks (m/z-intensity values) per spectrum. Returns an integer vector (length equal to the number of spectra). For empty spectra, 0 is returned.
msLevel: gets the spectra's MS level. Returns an integer vector (of length equal to the number of spectra) with the MS level for each spectrum (or NA_integer_ if not available).
mz: gets the mass-to-charge ratios (m/z) from the spectra. Returns a IRanges::NumericList() or length equal to the number of spectra, each element a numeric vector with the m/z values of one spectrum.
polarity, polarity<-: gets or sets the polarity for each spectrum. polarity returns an integer vector (length equal to the number of spectra), with 0 and 1 representing negative and positive polarities, respectively. polarity<- expects an integer vector of length 1 or equal to the number of spectra.
precursorCharge, precursorIntensity, precursorMz, precScanNum, precAcquisitionNum: get the charge (integer), intensity (numeric), m/z (numeric), scan index (integer) and acquisition number (interger) of the precursor for MS level 2 and above spectra from the object. Returns a vector of length equal to the number of spectra in object. NA are reported for MS1 spectra of if no precursor information is available.
reset: restores the backend to its original state, i.e. deletes all locally modified data and reinitializes the backend to the full data available in the database.
rtime, rtime<-: gets or sets the retention times for each spectrum (in seconds). rtime returns a numeric vector (length equal to the number of spectra) with the retention time for each spectrum. rtime<- expects a numeric vector with length equal to the number of spectra.
scanIndex: returns an integer vector with the scan index for each spectrum. This represents the relative index of the spectrum within each file. Note that this can be different to the acquisitionNum of the spectrum which is the index of the spectrum as reported in the mzML file.
selectSpectraVariables: reduces the information within the backend to the selected spectra variables.
smoothed,smoothed<-: gets or sets whether a spectrum is smoothed. smoothed returns a logical vector of length equal to the number of spectra. smoothed<- takes a logical vector of length 1 or equal to the number of spectra in object.
spectraData: gets general spectrum metadata (annotation, also called header). spectraData returns a DataFrame. Note that replacing the spectra data with spectraData<- is not supported.
spectraNames: returns a character vector with the names of the spectra in object.
spectraVariables: returns a character vector with the available spectra variables (columns, fields or attributes) available in object. This should return all spectra variables which are present in object, also "mz" and "intensity" (which are by default not returned by the spectraVariables,Spectra method).
tic: gets the total ion current/count (sum of signal of a spectrum) for all spectra in object. By default, the value reported in the original raw data file is returned. For an empty spectrum, NA_real_ is returned.

Not supported Backend functions

The following functions are not supported by the MsBackendMassbankSql since the original data can not be changed.

backendMerge, export, filterDataStorage, filterPrecursorScan, peaksData<-, filterAcquisitionNum, intensity<-, mz<-, precScanNum, spectraData<-, spectraNames<-.

Retrieving compound annotations for spectra

While compound annotations are also provided via the spectraVariables of the backend, it would also be possible to use the compounds function on a Spectra object (that uses a MsBackendMassbankSql backend) to retrieve compound annotations for the specific spectra.

Author

Johannes Rainer

Examples


## Create a connection to a database with MassBank data - in the present
## example we connect to a tiny SQLite database bundled in this package
## as public access to the MassBank MySQL is not (yet) supported. See the
## vignette for more information on how to install MassBank locally and
## enable MySQL database connections
library(RSQLite)
con <- dbConnect(SQLite(), system.file("sql", "minimassbank.sqlite",
    package = "MsBackendMassbank"))

## Given that we have the connection to a MassBank databas we can
## initialize the backend:
be <- backendInitialize(MsBackendMassbankSql(), dbcon = con)
be
#> MsBackendMassbankSql with 70 spectra
#>       msLevel precursorMz  polarity
#>     <integer>   <numeric> <integer>
#> 1           2         506         0
#> 2          NA          NA         1
#> 3          NA          NA         0
#> 4          NA          NA         1
#> 5          NA          NA         0
#> ...       ...         ...       ...
#> 66          2     185.028         0
#> 67          2     455.290         1
#> 68          2     253.051         0
#> 69          2     358.238         1
#> 70          2     256.170         1
#>  ... 41 more variables/columns.
#>  Use  'spectraVariables' to list all of them.

## Access MS level
msLevel(be)
#>  [1]  2 NA NA NA NA  2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA  2  2  2  2  2
#> [26]  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2
#> [51]  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2
be$msLevel
#>  [1]  2 NA NA NA NA  2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA  2  2  2  2  2
#> [26]  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2
#> [51]  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2

## Access m/z values
be$mz
#> NumericList of length 70
#> [[1]] 146.760803 158.863541 174.988785 ... 470.057434 487.989319 585.88446
#> [[2]] 22.99 23.07 23.19 38.98 53.15 60.08 ... 391.18 413.22 414.22 429.16 495.2
#> [[3]] 108.099566 152.005378 153.01824 ... 341.031964 409.06729 499.103447
#> [[4]] 137.0227 138.025605 139.034602 ... 304.271886 316.303106 352.234228
#> [[5]] 112.977759 205.053323 208.041128 ... 449.137152 671.1778 673.200866
#> [[6]] 78.893929 183.011719 193.957916 ... 328.091949 408.010193 426.021942
#> [[7]] 167.03389 168.040758 333.079965 ... 357.073039 365.040698 373.073473
#> [[8]] 195.09167 196.095033
#> [[9]] 108.096149 152.004656 153.01824 ... 359.997563 409.065314 491.043775
#> [[10]] 1278.12 1279.11 1279.18 1306.21 ... 2064.29 2091.32 2092.3 2136.33
#> ...
#> <60 more elements>

## Access the full spectra data (including m/z and intensity values)
spectraData(be)
#> DataFrame with 70 rows and 44 columns
#>       msLevel     rtime acquisitionNum scanIndex                             mz
#>     <integer> <numeric>      <integer> <integer>                  <NumericList>
#> 1           2        NA             NA        NA    146.761,158.864,174.989,...
#> 2          NA        NA             NA        NA          22.99,23.07,23.19,...
#> 3          NA        NA             NA        NA    108.100,152.005,153.018,...
#> 4          NA        NA             NA        NA    137.023,138.026,139.035,...
#> 5          NA        NA             NA        NA    112.978,205.053,208.041,...
#> ...       ...       ...            ...       ...                            ...
#> 66          2        NA             NA        NA                        185.028
#> 67          2        NA             NA        NA    58.0653,77.0386,79.0543,...
#> 68          2        NA             NA        NA    132.021,133.029,135.009,...
#> 69          2        NA             NA        NA    53.0388,54.0340,55.0544,...
#> 70          2        NA             NA        NA  88.0757,151.0540,152.0620,...
#>                                intensity dataStorage  dataOrigin centroided
#>                            <NumericList> <character> <character>  <logical>
#> 1     0.980184,938.145447, 56.718353,...  <MassBank>          NA         NA
#> 2                     3173,2266, 880,...  <MassBank>          NA         NA
#> 3                 2809,119550, 91935,...  <MassBank>          NA         NA
#> 4               157703, 23566,  5190,...  <MassBank>          NA         NA
#> 5                     5686, 927, 756,...  <MassBank>          NA         NA
#> ...                                  ...         ...         ...        ...
#> 66                              34967548  <MassBank>          NA         NA
#> 67           9143284, 341391,5278218,...  <MassBank>          NA         NA
#> 68         82825.8,290504.6,301494.3,...  <MassBank>          NA         NA
#> 69         1568742,19224644, 4676170,...  <MassBank>          NA         NA
#> 70          678846,  403851,11111366,...  <MassBank>          NA         NA
#>      smoothed  polarity precScanNum precursorMz precursorIntensity
#>     <logical> <integer>   <integer>   <numeric>          <numeric>
#> 1          NA         0          NA         506                408
#> 2          NA         1          NA          NA                 NA
#> 3          NA         0          NA          NA                 NA
#> 4          NA         1          NA          NA                 NA
#> 5          NA         0          NA          NA                 NA
#> ...       ...       ...         ...         ...                ...
#> 66         NA         0          NA     185.028            185.028
#> 67         NA         1          NA     455.290            455.290
#> 68         NA         0          NA     253.051            253.051
#> 69         NA         1          NA     358.238            358.237
#> 70         NA         1          NA     256.170            256.169
#>     precursorCharge collisionEnergy isolationWindowLowerMz
#>           <integer>       <numeric>              <numeric>
#> 1                NA              NA                     NA
#> 2                NA              NA                     NA
#> 3                NA              NA                     NA
#> 4                NA              NA                     NA
#> 5                NA              NA                     NA
#> ...             ...             ...                    ...
#> 66               NA              NA                     NA
#> 67               NA              NA                     NA
#> 68               NA              NA                     NA
#> 69               NA              NA                     NA
#> 70               NA              NA                     NA
#>     isolationWindowTargetMz isolationWindowUpperMz spectrum_id
#>                   <numeric>              <numeric> <character>
#> 1                        NA                     NA    MCH00020
#> 2                        NA                     NA    MCH00002
#> 3                        NA                     NA    MCH00006
#> 4                        NA                     NA    MCH00009
#> 5                        NA                     NA    MCH00014
#> ...                     ...                    ...         ...
#> 66                       NA                     NA    SM834451
#> 67                       NA                     NA    SM855703
#> 68                       NA                     NA    SM882851
#> 69                       NA                     NA    SM849703
#> 70                       NA                     NA    SM858801
#>              spectrum_name                   date                authors
#>                <character>            <character>            <character>
#> 1   Adenosine 5'-triphos.. 2016.01.19 (Created .. Yoshikuni K, Tajiri ..
#> 2   Gentisic acid; MALDI.. 2016.01.19 (Created .. Wada Y, Osaka Medica..
#> 3   Gentisic acid; MALDI.. 2016.01.19 (Created .. Wada Y, Osaka Medica..
#> 4   5-Methoxysalicylic a.. 2016.01.19 (Created .. Wada Y, Osaka Medica..
#> 5   Sinapic acid; MALDI-.. 2016.01.19 (Created .. Wada Y, Osaka Medica..
#> ...                    ...                    ...                    ...
#> 66  m-Xylene-4-sulfonic ..             2016.12.12 Krauss M, Schymanski..
#> 67  Verapamil; LC-ESI-QF..             2016.12.12 Krauss M, Schymanski..
#> 68  Daidzein; LC-ESI-QFT..             2016.12.12 Krauss M, Schymanski..
#> 69  Oxybutynin; LC-ESI-Q..             2016.12.12 Krauss M, Schymanski..
#> 70  Diphenhydramine; LC-.. 2019.11.20 (Created .. Krauss M, Schymanski..
#>         license              copyright            publication
#>     <character>            <character>            <character>
#> 1      CC BY-SA                     NA                     NA
#> 2      CC BY-SA                     NA                     NA
#> 3      CC BY-SA                     NA                     NA
#> 4      CC BY-SA                     NA                     NA
#> 5      CC BY-SA                     NA                     NA
#> ...         ...                    ...                    ...
#> 66        CC BY Copyright (C) 2016 U.. Schymanski, E. L.; R..
#> 67        CC BY Copyright (C) 2016 U.. Schymanski, E. L.; R..
#> 68        CC BY Copyright (C) 2016 U.. Schymanski, E. L.; R..
#> 69        CC BY Copyright (C) 2016 U.. Schymanski, E. L.; R..
#> 70        CC BY Copyright (C) 2016 U.. Schymanski, E. L.; R..
#>                     splash compound_id      adduct  ionization
#>                <character>   <integer> <character> <character>
#> 1   splash10-0a4i-000090..           1      [M-H]-          NA
#> 2   splash10-004r-191300..           2          NA          NA
#> 3   splash10-0udi-090200..           3          NA          NA
#> 4   splash10-0fri-093000..           4          NA          NA
#> 5   splash10-006t-019080..           5          NA          NA
#> ...                    ...         ...         ...         ...
#> 66  splash10-000i-090000..          66      [M-H]-         ESI
#> 67  splash10-066r-090030..          67      [M+H]+         ESI
#> 68  splash10-0udi-009000..          68      [M-H]-         ESI
#> 69  splash10-0a4i-860900..          69      [M+H]+         ESI
#> 70  splash10-014i-090000..          70      [M+H]+         ESI
#>     ionization_voltage fragmentation_mode             instrument
#>            <character>        <character>            <character>
#> 1                   NA                 NA LTQ Orbitrap XL, The..
#> 2                   NA                 NA Voyager DE-PRO, Appl..
#> 3                   NA                 NA Voyager DE-PRO, Appl..
#> 4                   NA                 NA Voyager DE-PRO, Appl..
#> 5                   NA                 NA Voyager DE-PRO, Appl..
#> ...                ...                ...                    ...
#> 66                  NA                HCD Q Exactive Plus Orbi..
#> 67                  NA                HCD Q Exactive Plus Orbi..
#> 68                  NA                HCD Q Exactive Plus Orbi..
#> 69                  NA                HCD Q Exactive Plus Orbi..
#> 70                  NA                HCD Q Exactive Plus Orbi..
#>     instrument_type       formula exactmass                 smiles
#>         <character>   <character> <numeric>            <character>
#> 1       LC-ESI-ITFT C10H16N5O13P3   506.996 Nc(n3)c(n2)c(nc3)n(c..
#> 2         MALDI-TOF        C7H6O4   154.027 Oc(c1)cc(C(O)=O)c(O)c1
#> 3         MALDI-TOF        C7H6O4   154.027 Oc(c1)cc(C(O)=O)c(O)c1
#> 4         MALDI-TOF        C8H8O4   168.042 COc(c1)cc(C(O)=O)c(O..
#> 5         MALDI-TOF      C11H12O5   224.068 COC1=CC(=CC(=C1O)OC)..
#> ...             ...           ...       ...                    ...
#> 66       LC-ESI-QFT      C8H10O3S   186.035 Cc1ccc(c(c1)C)S(=O)(..
#> 67       LC-ESI-QFT    C27H38N2O4   454.283 COc1ccc(CCN(C)CCCC(C..
#> 68       LC-ESI-QFT      C15H10O4   254.058 OC1=CC=C(C=C1)C1=COC..
#> 69       LC-ESI-QFT     C22H31NO3   357.230 CCN(CC)CC#CCOC(=O)C(..
#> 70       LC-ESI-QFT      C17H21NO   255.162 CN(C)CCOC(c1ccccc1)c..
#>                      inchi               inchikey         cas     pubchem
#>                <character>            <character> <character> <character>
#> 1   InChI=1S/C10H16N5O13.. ZKHQWZAMYRWXGA-KQYNX..     56-65-5    CID:5957
#> 2   InChI=1S/C7H6O4/c8-4.. WXTMDXOMEHJXQO-UHFFF..          NA    CID:3469
#> 3   InChI=1S/C7H6O4/c8-4.. WXTMDXOMEHJXQO-UHFFF..          NA    CID:3469
#> 4   InChI=1S/C8H8O4/c1-1.. IZZIWIAOVZOBLF-UHFFF..          NA   CID:75787
#> 5   InChI=1S/C11H12O5/c1.. PCMORTLOPMLEFB-ONEGZ..    530-59-6  CID:637775
#> ...                    ...                    ...         ...         ...
#> 66  InChI=1S/C8H10O3S/c1.. CHZLVSBMXZSPNN-UHFFF..     88-61-9    CID:6938
#> 67  InChI=1S/C27H38N2O4/.. SGTNSNPWRIOYBX-UHFFF..     52-53-9    CID:2520
#> 68  InChI=1S/C15H10O4/c1.. ZQSIJRDFPHDXIC-UHFFF..    486-66-8 CID:5281708
#> 69  InChI=1S/C22H31NO3/c.. XIQVNETUBQGFHX-UHFFF..   5633-20-5    CID:4634
#> 70  InChI=1S/C17H21NO/c1.. ZZVUWRFHKOJYTH-UHFFF..     58-73-1    CID:3100
#>                                                        synonym
#>                                                <CharacterList>
#> 1                                   Adenosine 5'-triphos..,ATP
#> 2                         2,5-Dihydroxybenzoic..,Gentisic acid
#> 3                     2,5-Dihydroxybenzoic..,DHB,Gentisic acid
#> 4                      5-Methoxysalicylic a..,DHBs (Super DHB)
#> 5   Sinapic acid,3,5-dimethoxy-4-hydr..,3-(4-hydroxy-3,5-dim..
#> ...                                                        ...
#> 66               m-Xylene-4-sulfonic ..,2,4-dimethylbenzenes..
#> 67                            Verapamil,2-(3,4-dimethoxyphen..
#> 68                             Daidzein,7-hydroxy-3-(4-hydro..
#> 69                           Oxybutynin,4-(diethylamino)but-..
#> 70                      Diphenhydramine,2-benzhydryloxy-N,N-..
#>     precursor_mz_text          compound_name
#>           <character>            <character>
#> 1          506.000000 Adenosine 5'-triphos..
#> 2                  NA 2,5-Dihydroxybenzoic..
#> 3                  NA 2,5-Dihydroxybenzoic..
#> 4                  NA 5-Methoxysalicylic a..
#> 5                  NA           Sinapic acid
#> ...               ...                    ...
#> 66           185.0278 m-Xylene-4-sulfonic ..
#> 67           455.2904              Verapamil
#> 68           253.0506               Daidzein
#> 69           358.2377             Oxybutynin
#> 70           256.1696        Diphenhydramine

## Add a new spectra variable
be$new_variable <- "b"
be$new_variable
#>  [1] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b"
#> [20] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b"
#> [39] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b"
#> [58] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b"

## Subset the backend
be_sub <- be[c(3, 1)]

spectraNames(be)
#>  [1] "MCH00020" "MCH00002" "MCH00006" "MCH00009" "MCH00014" "MCH00019"
#>  [7] "MCH00012" "MCH00003" "MCH00016" "MCH00001" "MCH00018" "MCH00007"
#> [13] "MCH00013" "MCH00015" "MCH00008" "MCH00004" "MCH00005" "MCH00011"
#> [19] "MCH00017" "MCH00010" "SM864952" "SM823851" "SM868004" "SM862204"
#> [25] "SM834302" "SM810352" "SM847101" "SM861203" "SM839603" "SM829401"
#> [31] "SM814501" "SM858902" "SM850104" "SM854403" "SM836003" "SM821703"
#> [37] "SM880602" "SM868101" "SM851552" "SM804503" "SM848503" "SM842251"
#> [43] "SM817703" "SM847302" "SM805801" "SM820101" "SM816753" "SM805001"
#> [49] "SM838051" "SM812904" "SM840401" "SM812701" "SM861901" "SM874401"
#> [55] "SM838502" "SM857001" "SM858203" "SM847702" "SM883903" "SM818403"
#> [61] "SM871101" "SM842156" "SM841901" "SM854306" "SM878551" "SM834451"
#> [67] "SM855703" "SM882851" "SM849703" "SM858801"
spectraNames(be_sub)
#> [1] "MCH00006" "MCH00020"