List of Spectrum objects along with annotations

MSpectra (Mass Spectra) objects allow to collect one or more Spectrum object(s) (Spectrum1 or Spectrum2) in a list-like structure with the possibility to add arbitrary annotations to each individual Spectrum object. These can be accessed/set with the mcols() method.

MSpectra objects can be created with the MSpectra function.

Functions to access the individual spectra's attributes are available (listed below).

writeMgfData exports a MSpectra object to a file in MGF format. All metadata columns present in mcols are exported as additional fields with the capitalized column names used as field names (see examples below).

Usage

MSpectra(..., elementMetadata = NULL)

# S4 method for class 'MSpectra'
mz(object)

# S4 method for class 'MSpectra'
intensity(object)

# S4 method for class 'MSpectra'
rtime(object)

# S4 method for class 'MSpectra'
precursorMz(object)

# S4 method for class 'MSpectra'
precursorCharge(object)

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

# S4 method for class 'MSpectra'
precursorIntensity(object)

# S4 method for class 'MSpectra'
acquisitionNum(object)

# S4 method for class 'MSpectra'
scanIndex(object)

# S4 method for class 'MSpectra,ANY'
peaksCount(object)

# S4 method for class 'MSpectra'
msLevel(object)

# S4 method for class 'MSpectra'
tic(object)

# S4 method for class 'MSpectra'
ionCount(object)

# S4 method for class 'MSpectra'
collisionEnergy(object)

# S4 method for class 'MSpectra'
fromFile(object)

# S4 method for class 'MSpectra'
polarity(object)

# S4 method for class 'MSpectra'
smoothed(object)

# S4 method for class 'MSpectra'
isEmpty(x)

# S4 method for class 'MSpectra'
centroided(object)

# S4 method for class 'MSpectra'
isCentroided(object)

# S4 method for class 'MSpectra'
writeMgfData(object, con = "spectra.mgf", COM = NULL, TITLE = NULL)

# S4 method for class 'MSpectra'
clean(object, all = FALSE, msLevel. = msLevel., ...)

# S4 method for class 'MSpectra'
removePeaks(object, t, msLevel., ...)

# S4 method for class 'MSpectra'
filterMz(object, mz, msLevel., ...)

# S4 method for class 'MSpectra'
pickPeaks(
  object,
  halfWindowSize = 3L,
  method = c("MAD", "SuperSmoother"),
  SNR = 0L,
  refineMz = c("none", "kNeighbors", "kNeighbours", "descendPeak"),
  msLevel. = unique(msLevel(object)),
  ...
)

# S4 method for class 'MSpectra'
smooth(
  x,
  method = c("SavitzkyGolay", "MovingAverage"),
  halfWindowSize = 2L,
  ...
)

# S4 method for class 'MSpectra'
filterMsLevel(object, msLevel.)

Arguments

...: For MSpectra: Spectrum object(s) or a list of Spectrum objects. For all other methods optional arguments passed along.
elementMetadata: For MSpectra: DataFrame with optional information that should be added as metadata information (mcols) to the object. The number of rows has to match the number of Spectrum objects, each row is expected to represent additional metadata information for one spectrum.
object: For all functions: a MSpectra object.
x: For all functions: a MSpectra object.
con: For writeMgfData: character(1) defining the file name of the MGF file.
COM: For writeMgfData: optional character(1) providing a comment to be added to the file.
TITLE: For writeMgfData: optional character(1) defining the title for the MGF file.
all: For clean: if FALSE original 0-intensity values are retained around peaks.
msLevel.: For clean, removePeaks, filterMz, pickPeaks: optionally specify the MS level(s) of the spectra on which the operation should be performed. For filterMsLevels: MS level(s) to which the MSpectra should be reduced.
t: For removePeaks: numeric(1) specifying the threshold below which intensities are set to 0.
mz: For filterMz: numeric(2) defining the lower and upper m/z for the filter. See filterMz() for details.
halfWindowSize: For pickPeaks and smooth: see pickPeaks() and smooth() for details.
method: For pickPeaks and smooth: see pickPeaks() and smooth() for details.
SNR: For pickPeaks: see pickPeaks() for details.
refineMz: For pickPeaks: see pickPeaks() for details.

Details

MSpectra inherits all methods from the SimpleList class of the S4Vectors package. This includes lapply and other data manipulation and subsetting operations.

Constructor

New MSpectra can be created with the MSpectra(...) function where ... can either be a single Spectrum object or a list of Spectrum objects (Spectrum1 and/or Spectrum2).

Accessing spectrum attributes

These methods allow to access the attributes and values of the individual Spectrum (Spectrum1 or Spectrum2) objects within the list.

mz return the m/z values of each spectrum as a list of numeric vectors.
intensity return the intensity values of each spectrum as a list of numeric vectors.
rtime return the retention time of each spectrum as a numeric vector with length equal to the length of object.
precursorMz, precursorCharge, precursorIntensity, precScanNum return precursor m/z values, charge, intensity and scan number for each spectrum as a numeric (or integer) vector with length equal to the length of object. Note that for Spectrum1 objects NA will be returned.
acquisitionNum and scanIndex return the acquisition number of each spectrum and its scan index as an integer vector with the same length than object.
ionCount and tic return the ion count and total ion current of each spectrum.
peaksCount returns the number of peaks for each spectrum as a integer vector.
msLevel returns the MS level of each spectrum.
collisionEnergy returns the collision energy for each spectrum or NA for Spectrum1 objects.
polarity returns the spectra's polarity.
fromFile returns the index from the (e.g. mzML) file the spectra where from. This applies only for spectra read using the readMSData() function.
smoothed whether spectra have been smoothed (i.e. processed with the smooth() method. Returns a logical of length equal to the number of spectra.
isEmpty returns TRUE for spectra without peak data.
centroided, isCentroided returns for each spectrum whether it contains centroided data. While centroided returns the internal attribute of each spectrum, isCentroided tries to guess whether spectra are centroided from the actual peak data.

Data manipulation methods

clean cleans each spectrum. See clean() for more details.
pickPeaks performs peak picking to generate centroided spectra. See pickPeaks() for more details.
removePeaks removes peaks lower than a threshold t. See removePeaks() for more details.
smooth smooths spectra. See smooth() for more details.

Filtering and subsetting

[ can be used to subset the MSpectra object.
filterMsLevel filters MSpectra to retain only spectra from certain MS level(s).
filterMz filters the spectra by the specified mz range. See filterMz() for details.

Author

Johannes Rainer

Examples


## Create from Spectrum objects
sp1 <- new("Spectrum1", mz = c(1, 2, 4), intensity = c(4, 5, 2))
sp2 <- new("Spectrum2", mz = c(1, 2, 3, 4), intensity = c(5, 3, 2, 5),
    precursorMz = 2)

spl <- MSpectra(sp1, sp2)
spl
#> MSpectra with 2 spectra and 0 metadata column(s):
#>       msLevel     rtime peaksCount
#>     <integer> <numeric>  <integer>
#>   1         1        NA          3
#>   2         2        NA          4
spl[[1]]
#> Object of class "Spectrum1"
#>  MSn level: 1 
#>  Total ion count: 3 
#>  Polarity:  

## Add also metadata columns
mcols(spl)$id <- c("a", "b")
mcols(spl)
#> DataFrame with 2 rows and 1 column
#>            id
#>   <character>
#> 1           a
#> 2           b

## Create a MSpectra with metadata
spl <- MSpectra(sp1, sp2, elementMetadata = DataFrame(id = c("a", "b")))

mcols(spl)
#> DataFrame with 2 rows and 1 column
#>            id
#>   <character>
#> 1           a
#> 2           b
mcols(spl)$id
#> [1] "a" "b"

## Extract the mz values for the individual spectra
mz(spl)
#> $`1`
#> [1] 1 2 4
#> 
#> $`2`
#> [1] 1 2 3 4
#> 

## Extract the intensity values for the individual spectra
intensity(spl)
#> $`1`
#> [1] 4 5 2
#> 
#> $`2`
#> [1] 5 3 2 5
#> 

## Extract the retention time values for the individual spectra
rtime(spl)
#>  1  2 
#> NA NA 

## Extract the precursor m/z of each spectrum.
precursorMz(spl)
#>  1  2 
#> NA  2 

## Extract the precursor charge of each spectrum.
precursorCharge(spl)
#>  1  2 
#> NA NA 

## Extract the precursor scan number for each spectrum.
precScanNum(spl)
#>  1  2 
#> NA NA 

## Extract the precursor intensity of each spectrum.
precursorIntensity(spl)
#>  1  2 
#> NA NA 

## Extract the acquisition number of each spectrum.
acquisitionNum(spl)
#>  1  2 
#> NA NA 

## Extract the scan index of each spectrum.
scanIndex(spl)
#>  1  2 
#> NA NA 

## Get the number of peaks per spectrum.
peaksCount(spl)
#> 1 2 
#> 3 4 

## Get the MS level of each spectrum.
msLevel(spl)
#> 1 2 
#> 1 2 

## Get the total ion current for each spectrum.
tic(spl)
#>  1  2 
#> 11 15 

## Get the total ion current for each spectrum.
ionCount(spl)
#>  1  2 
#> 11 15 

## Extract the collision energy for each spectrum.
collisionEnergy(spl)
#>  1  2 
#> NA NA 

## Extract the file index for each spectrum.
fromFile(spl)
#>  1  2 
#> NA NA 

## Get the polarity for each spectrum.
polarity(spl)
#>  1  2 
#> NA NA 

## Whether spectra are smoothed (i.e. processed with the `smooth`
## function).
smoothed(spl)
#>  1  2 
#> NA NA 

## Are spectra empty (i.e. contain no peak data)?
isEmpty(spl)
#>     1     2 
#> FALSE FALSE 

## Do the spectra contain centroided data?
centroided(spl)
#>  1  2 
#> NA NA 

## Do the spectra contain centroided data? Whether spectra are centroided
## is estimated from the peak data.
isCentroided(spl)
#>  1  2 
#> NA NA 

## Export the spectrum list to a MGF file. Values in metadata columns are
## exported as additional field for each spectrum.
tmpf <- tempfile()
writeMgfData(spl, tmpf)

## Evaluate the written output. The ID of each spectrum (defined in the
## "id" metadata column) is exported as field "ID".
readLines(tmpf)
#>  [1] "COM=Experimentexported by MSnbase on Tue Oct 15 15:25:57 2024"   
#>  [2] "BEGIN IONS"                                                      
#>  [3] "SCANS=NA"                                                        
#>  [4] "TITLE=msLevel 1; retentionTime ; scanNum NA"                     
#>  [5] "RTINSECONDS="                                                    
#>  [6] "ID=a"                                                            
#>  [7] "1 4"                                                             
#>  [8] "2 5"                                                             
#>  [9] "4 2"                                                             
#> [10] "END IONS"                                                        
#> [11] ""                                                                
#> [12] "BEGIN IONS"                                                      
#> [13] "SCANS="                                                          
#> [14] "TITLE=msLevel 2; retentionTime ; scanNum ; precMz 2; precCharge "
#> [15] "RTINSECONDS="                                                    
#> [16] "PEPMASS=2"                                                       
#> [17] "ID=b"                                                            
#> [18] "1 5"                                                             
#> [19] "2 3"                                                             
#> [20] "3 2"                                                             
#> [21] "4 5"                                                             
#> [22] "END IONS"                                                        

## Set mcols to NULL to avoid export of additional data fields.
mcols(spl) <- NULL
file.remove(tmpf)
#> [1] TRUE

writeMgfData(spl, tmpf)
readLines(tmpf)
#>  [1] "COM=Experimentexported by MSnbase on Tue Oct 15 15:25:57 2024"   
#>  [2] "BEGIN IONS"                                                      
#>  [3] "SCANS=NA"                                                        
#>  [4] "TITLE=msLevel 1; retentionTime ; scanNum NA"                     
#>  [5] "RTINSECONDS="                                                    
#>  [6] "1 4"                                                             
#>  [7] "2 5"                                                             
#>  [8] "4 2"                                                             
#>  [9] "END IONS"                                                        
#> [10] ""                                                                
#> [11] "BEGIN IONS"                                                      
#> [12] "SCANS="                                                          
#> [13] "TITLE=msLevel 2; retentionTime ; scanNum ; precMz 2; precCharge "
#> [14] "RTINSECONDS="                                                    
#> [15] "PEPMASS=2"                                                       
#> [16] "1 5"                                                             
#> [17] "2 3"                                                             
#> [18] "3 2"                                                             
#> [19] "4 5"                                                             
#> [20] "END IONS"                                                        

## Filter the object by MS level
filterMsLevel(spl, msLevel. = 1)
#> MSpectra with 1 spectra and 0 metadata column(s):
#>       msLevel     rtime peaksCount
#>     <integer> <numeric>  <integer>
#>   1         1        NA          3