MS2ID class for high-throughput MS/MS annotation

The `MS2ID` class encapsulates, a MS2 spectra database along with its metadata. Its internal structure allows to annotate query spectra - with the annotate function - using big spectra databases at high speed and low RAM requirements (typically 100 query spectra/min against a 1M5 spectra library). MS2ID class uses a SQLite database with the metadata and bigmemory files to store the spectra (i.e. peaks matrices) and their mass-charge index. See vignette.

createMS2ID processes the data contained in a CompDb object (Stanstrup and Rainer 2021) and creates a MS2ID backend by saving data as SQL and bigMemory files in a directory. Later on, that directory will be load as an MS2ID object in order to be used repeatedly as reference library with the annotate function.

MS2ID(ms2idFolder)

# S4 method for MS2ID
show(object)

createMS2ID(
  name = "MS2ID",
  path = ".",
  cmpdb,
  noiseThresh = 0.01,
  calcSplash = TRUE,
  calcMmi = TRUE,
  overwrite = FALSE
)

Arguments

ms2idFolder	character(1) with the directory's path of the MS2ID backend
object	character: signature supported
name	character(1) name of the directory where the files will be saved.
path	character(1) with the path where to create the MS2ID backend.
cmpdb	`CompDb`(1) object (with MS/MS spectra).
noiseThresh	A numeric defining the threshold used in the noise filtering of the MS/MS spectra. e.g. noiseThresh = 0.01 removes peaks with an intensity less than 1% of the base peak.
calcSplash	boolean(1) indicating if SPLASH values (when missing) must be calculated using the `getSplash` function.
calcMmi	boolean(1) indicating if compound monoisotopic mass values (when missing) must be calculated using the `check_chemform` function.
overwrite	boolean(1) indicating if the function can overwrite results.

Value

createMS2ID returns a character(1) with the MS2ID backend location. This value must be used as ms2idFolder parameter in the MS2ID constructor.

Details

The createMS2ID function creates a MS2ID backend that is subsequently used by the MS2ID constructor, which creates the MS2ID object.

General functions

createMS2ID(): Function to create MS2ID backends.
MS2ID(): Constructor function for MS2ID objects.

References

Stanstrup J, Rainer J (2021). CompoundDb: Creating and Using (Chemical) Compound Annotation Databases. R package version 0.8.1, https://github.com/EuracBiomedicalResearch/CompoundDb.

Author

Josep M. Badia josepmaria.badia@urv.cat

Examples

## OBTAIN MS2ID LIBRARY ---
## Decompress the MoNA subset that comes with MS2ID
MoNAsubset <- system.file("extdata/MoNAsubset.sdf.gz",
                          package = "MS2ID")
## Use CompoundDB to parse MoNA
library(CompoundDb)
#> Error in library(CompoundDb): there is no package called ‘CompoundDb’
cmps <- suppressWarnings(compound_tbl_sdf(MoNAsubset))
#> Error in compound_tbl_sdf(MoNAsubset): could not find function "compound_tbl_sdf"
spctr <- msms_spectra_mona(MoNAsubset, collapsed = TRUE)
#> Error in msms_spectra_mona(MoNAsubset, collapsed = TRUE): could not find function "msms_spectra_mona"
spctr$predicted <- FALSE
#> Error in spctr$predicted <- FALSE: object 'spctr' not found
metad <- data.frame(
    name = c("source", "url",
             "source_version","source_date"),
    value = c("MoNA",
              "https://mona.fiehnlab.ucdavis.edu/downloads",
              "v1", '07-09')
)
cmpdbDir <- file.path(tempdir(), "cmpdbDir")
if(dir.exists(cmpdbDir)){
    do.call(file.remove,
            list(list.files(cmpdbDir, full.names = TRUE)))
}else{
    dir.create(cmpdbDir)
}
db_file <- createCompDb(cmps, metadata = metad,
                        msms_spectra = spctr,
                        path = cmpdbDir)
#> Error in createCompDb(cmps, metadata = metad, msms_spectra = spctr, path = cmpdbDir): could not find function "createCompDb"
cmpdb <- CompDb(db_file)
#> Error in CompDb(db_file): could not find function "CompDb"
## Create the MS2ID backend
library(MS2ID)
MS2IDdirectory <- createMS2ID(cmpdb = cmpdb,
                              overwrite = TRUE, path = tempdir())
#> Error in is(cmpdb, "CompDb"): object 'cmpdb' not found
## Obtain the MS2ID object
MS2IDlib <- MS2ID(MS2IDdirectory)
#> Error in file.exists(ms2idFolder): object 'MS2IDdirectory' not found