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Class to store data from a loaded MS library

Source: R/generics.R, R/mslibrary.R
MSLibrary-class.Rd

Stores the spectra and metadata from the records of an MS library.

Usage

records(obj)

spectra(obj)

# S4 method for class 'MSLibrary'
records(obj)

# S4 method for class 'MSLibrary'
spectra(obj)

# S4 method for class 'MSLibrary'
length(x)

# S4 method for class 'MSLibrary'
names(x)

# S4 method for class 'MSLibrary'
show(object)

# S4 method for class 'MSLibrary,ANY,missing,missing'
x[i, j, ..., drop = TRUE]

# S4 method for class 'MSLibrary,ANY,missing'
x[[i, j]]

# S4 method for class 'MSLibrary'
x$name

# S4 method for class 'MSLibrary'
as.data.table(x)

# S4 method for class 'MSLibrary'
delete(obj, i = NULL, j = NULL, ...)

# S4 method for class 'MSLibrary'
filter(
  obj,
  properties = NULL,
  massRange = NULL,
  mzRangeSpec = NULL,
  relMinIntensity = NULL,
  topMost = NULL,
  onlyAnnotated = FALSE,
  negate = FALSE
)

# S4 method for class 'MSLibrary'
convertToSuspects(
  obj,
  adduct,
  spectrumType = "MS2",
  avgSpecParams = getDefAvgPListParams(minIntensityPre = 0, minIntensityPost = 2, topMost
    = 10),
  collapse = TRUE,
  suspects = NULL,
  prefCalcChemProps = TRUE,
  neutralChemProps = FALSE
)

# S4 method for class 'MSLibrary'
export(obj, type = "msp", out)

# S4 method for class 'MSLibrary,MSLibrary'
merge(x, y, ...)

Arguments

x, obj, object

MSLibrary object to be accessed.

i

For [/[[: A numeric or character value which is used to select records by their index or name, respectively (for the order/names see names()).

For [: Can also be logical to perform logical selection (similar to regular vectors). If missing all records are selected.

For [[: should be a scalar value.

...

Unused.

drop, j

ignored.

name

The record name (partially matched).

properties

A named list with properties to be filtered. Each item in the list should be named with the name of the property, and should be a vector with allowed values. To obtain the possible properties, run e.g. names(records). Example: properties=list(Instrument_type=c("LC-ESI-QTOF","LC-ESI-TOF")). Set to NULL to ignore.

massRange

Records with a neutral mass outside this range will be removed. Should be a two-sized numeric vector with the lower and upper mass range. Set to NULL to ignore.

mzRangeSpec

Similar to the massRange argument, but removes any peaks from recorded mass spectra outside the given m/z range.

relMinIntensity

The minimum relative intensity (0-1) of a mass peak to be kept. Set to NULL to ignore.

topMost

Only keep topMost number of mass peaks for each spectrum. This filter is applied after others. Set to NULL to ignore.

onlyAnnotated

If TRUE then only recorded spectra that are formula annotated are kept.

negate

If TRUE then filters are performed in opposite manner.

adduct

An adduct object (or something that can be converted to it with as.adduct). Any records with a different adduct (Precursor_type) are not considered. Alternatively, adduct can be set to NULL to not filter out any records. However, in this case no MS/MS fragments will be added to the returned suspect list.

spectrumType

A character vector which limits library records to the given spectrum types (Spectrum_type field, e.g. "MS2"). Set to NULL to allow all spectrum types.

avgSpecParams

A list with parameters used for averaging spectra. See getDefAvgPListParams for more details.

collapse

Whether records with the same first-block InChIKey should be collapsed. See the Suspect conversion section for details.

suspects

If not NULL then this should be a suspect list (see screenSuspects) which will be amended with spectra data. See the Suspect conversion section for details.

prefCalcChemProps

If TRUE then calculated chemical properties such as the formula and InChIKey are preferred over what is already present in the input suspect list to convertToSuspects. For efficiency reasons it is recommended to set this to TRUE. See the Validating and calculating chemical properties section for more details.

neutralChemProps

If TRUE then the neutral form of the molecule is considered to calculate SMILES, formulae etc. Enabling this may improve feature matching when considering common adducts (e.g. [M+H]+, [M-H]-). See the Validating and calculating chemical properties section for more details.

type

The export type. Currently just "msp".

out

The file path to the output library file.

y

The MSLibrary to be merged with x.

Value

delete returns the object for which the specified data was removed.

filter returns a filtered MSLibrary object.

convertToSuspects return a suspect list (data.table), which can be used with screenSuspects.

merge returns a merged MSLibrary object.

Details

This class is used by loadMSLibrary to store the loaded MS library data.

Methods (by generic)

  • records(MSLibrary): Accessor method for the records slot of an MSLibrary class.

  • spectra(MSLibrary): Accessor method for the spectra slot of an MSLibrary class.

  • length(MSLibrary): Obtains the total number of records stored.

  • names(MSLibrary): Obtains the names of the stored records (DB_ID field).

  • show(MSLibrary): Shows summary information for this object.

  • x[i: Subset on records.

  • x[[i: Extracts a spectrum table for a record.

  • $: Extracts a spectrum table for a record.

  • as.data.table(MSLibrary): Converts all the data (spectra and metadata) to a single data.table.

  • delete(MSLibrary): Completely deletes specified full records or spectra.

  • filter(MSLibrary): Performs rule-based filtering of records and spectra. This may be especially to improve annotation with generateCompoundsLibrary.

  • convertToSuspects(MSLibrary): Converts the MS library data to a suspect list, which can be used with screenSuspects. See the Suspect conversion section for details.

  • export(MSLibrary): Exports the library data to a .msp file. The export is accelerated by an C++ interface with Rcpp.

  • merge(x = MSLibrary, y = MSLibrary): Merges two MSLibrary objects (x and y). The records from y that are unique are added to x. Records that were already in x are simply ignored. The SPLASH values are used to test equality between records, hence, the calcSPLASH argument to loadMSLibrary should be TRUE.

Slots

records

A data.table with metadata for all records. Use the records method for access.

spectra

A list with all (annotated) spectra. Each spectrum is stored in a data.table. Use the spectra method for access.

Note

export does not split any Synon data that was merged when the library was loaded.

S4 class hierarchy

Suspect conversion

The convertToSuspects method converts MS library data to a suspect list, which can be used with e.g. screenSuspects. Furthermore, this function can also amend existing suspect lists with spectral data.

Conversion occurs in either of the following three methods:

  1. Direct (collapse=FALSE and suspects=NULL): each record is considered a suspect, and the resulting suspect list is generated directly by converting the records metadata. The fragments_mz column for each suspect is constructed from the mass peaks of the corresponding record.

  2. Collapse (collapse=TRUE and suspects=NULL): All records with the same first-block InChIKey are first merged, and their spectra are averaged using the parameters from the avgSpecParams argument (see getDefAvgPListParams). The suspect list is based on the merged records, where the fragments_mz column is constructed from the averaged spectra. This is generally a good default, especially with large MS libraries.

  3. Amend (suspects is not NULL): only those records are considered if their first-block InChIKey is present in the suspect list. The remaining records and their spectra are then collapsed as described for the Collapse method, and the fragments_mz column for each suspect is set from the averaged spectra. If a suspect is not present in the library, its fragments_mz value will be empty. Note that any existing fragments_mz data will be overwritten.

Validating and calculating chemical properties

Chemical properties such as SMILES, InChIKey and formulae in the input suspect list to convertToSuspects are automatically validated and calculated if missing/invalid.

The internal validation/calculation process performs the following steps:

  • Validation of SMILES, InChI, InChIKey and formula data (if present). Invalid entries will be set to NA.

  • If neutralChemProps=TRUE then chemical data (SMILES, formulae etc.) is neutralized by (de-)protonation (using the –neutralized option of OpenBabel). An additional column molNeutralized is added to mark those molecules that were neutralized. Note that neutralization requires either SMILES or InChI data to be available.

  • The SMILES and InChI data are used to calculate missing or invalid SMILES, InChI, InChIKey and formula data. If prefCalcChemProps=TRUE then existing InChIKey and formula data is overwritten by calculated values whenever possible.

  • The chemical formulae which were not calculated are verified and normalized. This process may be time consuming, and is potentially largely avoided by setting prefCalcChemProps=TRUE.

  • Neutral masses are calculated for missing values (prefCalcChemProps=FALSE) or whenever possible (prefCalcChemProps=TRUE).

Note that calculation of formulae for molecules that are isotopically labelled is currently only supported for deuterium (2H) elements.

This functionality relies heavily on OpenBabel, please make sure it is installed.

References

Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O (2016). “SPLASH, a hashed identifier for mass spectra.” Nature Biotechnology, 34(11), 1099–1101. doi:10.1038/nbt.3689 .

Eddelbuettel D (2013). Seamless R and C++ Integration with Rcpp. Springer, New York. doi:10.1007/978-1-4614-6868-4 . ISBN 978-1-4614-6867-7.

Eddelbuettel D, Balamuta J (2018). “Extending R with C++: A Brief Introduction to Rcpp.” The American Statistician, 72(1), 28-36. doi:10.1080/00031305.2017.1375990 .

Eddelbuettel D, François R (2011). “Rcpp: Seamless R and C++ Integration.” Journal of Statistical Software, 40(8), 1–18. doi:10.18637/jss.v040.i08 .

Eddelbuettel D, Francois R, Allaire J, Ushey K, Kou Q, Russell N, Ucar I, Bates D, Chambers J (2026). Rcpp: Seamless R and C++ Integration. R package version 1.1.2, https://www.rcpp.org.

OBoyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011). “Open Babel: An open chemical toolbox.” Journal of Cheminformatics, 3(1). doi:10.1186/1758-2946-3-33 .

See also

loadMSLibrary