The OnDiskMSnExp Class for MS Data And Meta-Data — OnDiskMSnExp-class • MSnbase

Like the MSnExp class, the OnDiskMSnExp class encapsulates data and meta-data for mass spectrometry experiments, but does, in contrast to the former, not keep the spectrum data in memory, but fetches the M/Z and intensity values on demand from the raw files. This results in some instances to a reduced performance, has however the advantage of a much smaller memory footprint.

Details

The OnDiskMSnExp object stores many spectrum related information into the featureData, thus, some calls, like rtime to retrieve the retention time of the individual scans does not require the raw data to be read. Only M/Z and intensity values are loaded on-the-fly from the original files. Extraction of values for individual scans is, for mzML files, very fast. Extraction of the full data (all spectra) are performed in a per-file parallel processing strategy.

Data manipulations related to spectras' M/Z or intensity values (e.g. removePeaks or clean) are (for OnDiskMSnExp objects) not applied immediately, but are stored for later execution into the spectraProcessingQueue. The manipulations are performed on-the-fly upon data retrieval. Other manipulations, like removal of individual spectra are applied directly, since the corresponding data is available in the object's featureData slot.

Objects from the Class

Objects can be created by calls of the form new("OnDiskMSnExp",...). However, it is preferred to use the readMSData function with argument backend="disk" that will read raw mass spectrometry data to generate a valid "OnDiskMSnExp" instance.

Slots

backend:: Character string specifying the used backend.
spectraProcessingQueue:: list of ProcessingStep objects defining the functions to be applied on-the-fly to the spectra data (M/Z and intensity duplets).
assayData:: Object of class "environment" that is however empty, as no spectrum data is stored. Slot is inherited from "pSet".
phenoData:: Object of class "AnnotatedDataFrame" containing experimenter-supplied variables describing sample (i.e the individual tags for an labelled MS experiment) See phenoData for more details. Slot is inherited from "pSet".
featureData:: Object of class "AnnotatedDataFrame" containing variables describing features (spectra in our case). See featureData for more details. Slot is inherited from "pSet".
experimentData:: Object of class "MIAPE", containing details of experimental methods. See experimentData for more details. Slot is inherited from "pSet".
protocolData:: Object of class "AnnotatedDataFrame" containing equipment-generated variables (inherited from "eSet"). See protocolData for more details. Slot is inherited from "pSet".
processingData:: Object of class "MSnProcess" that records all processing. Slot is inherited from "pSet".
.__classVersion__:: Object of class "Versions" describing the versions of R, the Biobase package, "pSet" and MSnExp of the current instance. Slot is inherited from "pSet". Intended for developer use and debugging (inherited from "eSet").

Extends

Class "MSnExp", directly. Class "pSet", by class "MSnExp", distance 3. Class "VersionedBiobase", by class "pSet", distance 4. Class "Versioned", by class "pSet", distance 5.

Getter/setter methods

(in alphabetical order) See also methods for MSnExp or pSet objects.

[

object[i]:subset the OnDiskMSnExp by spectra. i can be a numeric or logical vector specifying to which spectra the data set should be reduced (with i being the index of the spectrum in the object's featureData).

The method returns a OnDiskMSnExp object with the data sub-set.

[[

object[[i]]: extract s single spectrum from the OnDiskMSnExp object object. Argument i can be either numeric or character specifying the index or the name of the spectrum in the object (i.e. in the featureData). The relevant information will be extracted from the corresponding raw data file.

The method returns a Spectrum1 object.

acquisitionNum

acquisitionNum(signature(object="OnDiskMSnExp")): get the acquisition number of each spectrum in each individual file. The relevant information is extracted from the object's featureData slot.

Returns a numeric vector with names corresponding to the spectrum names.

assayData

assayData(signature(object = "OnDiskMSnExp")): Extract the full data, i.e. read all spectra from the original files, apply all processing steps from the spectraProcessingQueue slot and return the data. Due to the required processing time accessing the full data should be avoided wherever possible.

Returns an environment.

centroided,centroided<-

centroided(signature(object="OnDiskMSnExp", msLevel, = "numeric")): whether individual spectra are centroided or uncentroided. The relevant information is extracted from the object's featureData slot. Returns a logical vector with names corresponding to the spectrum names. Use centroided(object) <- value to update the information, with value being a logical vector of length equal to the number of spectra in the experiment.

isCentroided(object, k = 0.025, qtl = 0.9, verbose = TRUE)

A heuristic assessing if the spectra in the object are in profile or centroided mode. The function takes the qtlth quantile top peaks, then calculates the difference between adjacent M/Z value and returns TRUE if the first quartile is greater than k. (See MSnbase:::.isCentroided for the code.) If verbose (default), a table indicating mode for all MS levels is printed.

The function has been tuned to work for MS1 and MS2 spectra and data centroided using different peak picking algorithms, but false positives can occur. See https://github.com/lgatto/MSnbase/issues/131 for details. For whole experiments, where all MS1 and MS2 spectra are expected to be in the same, albeit possibly different modes, it is advised to assign the majority result for MS1 and MS2 spectra, rather than results for individual spectra.

See also isCentroidedFromFile that accessed the mode directly from the raw data file.

fromFile

fromFile(signature(object = "OnDiskMSnExp")): get the index of the file (in fileNames(object)) from which the spectra were read. The relevant information is extracted from the object's featureData slot.

Returns a numeric vector with names corresponding to the spectrum names.

intensity

intensity(signature(object="OnDiskMSnExp")): return the intensities from each spectrum in the data set. Intensities are first read from the raw files followed by an optional processing (depending on the processing steps defined in the spectraProcessingQueue). To reduce the amount of required memory, this is performed on a per-file basis. The BPPARAM argument allows to specify how and if parallel processing should be used. Information from individual files will be processed in parallel (one process per original file).

The method returns a list of numeric intensity values. Each list element represents the intensities from one spectrum.

ionCount

ionCount(signature(object="OnDiskMSnExp", BPPARAM=bpparam())): extract the ion count (i.e. sum of intensity values) for each spectrum in the data set. The relevant data has to be extracted from the raw files (with eventually applying processing steps). The BPPARAM argument can be used to define how and if parallel processing should be used. Information from individual files will be processed in parallel (one process per original file).

Returns a numeric vector with names corresponding to the spectrum names.

isolationWindowLowerMz

isolationWindowLowerMz(object = "OnDiskMSnExp"): return the lower m/z boundary for the isolation window.

Returns a numeric vector of length equal to the number of spectra with the lower m/z value of the isolation window or NA if not specified in the original file.

isolationWindowUpperMz

isolationWindowUpperMz(object = "OnDiskMSnExp"): return the upper m/z boundary for the isolation window.

Returns a numeric vector of length equal to the number of spectra with the upper m/z value of the isolation window or NA if not specified in the original file.

length

length(signature(object="OnDiskMSnExp")): Returns the number of spectra of the current experiment.

msLevel

msLevel(signature(object = "OnDiskMSnExp")): extract the MS level from the spectra. The relevant information is extracted from the object's featureData slot.

Returns a numeric vector with names corresponding to the spectrum names.

mz

mz(signature(object="OnDiskMSnExp")): return the M/Z values from each spectrum in the data set. M/Z values are first read from the raw files followed by an optional processing (depending on the processing steps defined in the spectraProcessingQueue). To reduce the amount of required memory, this is performed on a per-file basis. The BPPARAM argument allows to specify how and if parallel processing should be used. Information from individual files will be processed in parallel (one process per original file).

The method returns a list of numeric M/Z values. Each list element represents the values from one spectrum.

peaksCount

peaksCount(signature(object="OnDiskMSnExp", scans="numeric"), BPPARAM=bpparam()): extrac the peaks count from each spectrum in the object. Depending on the eventually present ProcessingStep objects in the spectraProcessingQueue raw data will be loaded to calculate the peaks count. If no steps are present, the data is extracted from the featureData. Optional argument scans allows to specify the index of specific spectra from which the count should be returned. The BPPARAM argument can be used to define how and if parallel processing should be used. Information from individual files will be processed in parallel (one process per original file).

Returns a numeric vector with names corresponding to the spectrum names.

polarity

polarity(signature(object="OnDiskMSnExp")): returns a numeric vector with the polarity of the individual spectra in the data set. The relevant information is extracted from the featureData.

rtime

rtime(signature(object="OnDiskMSnExp")): extrac the retention time of the individual spectra in the data set (from the featureData).

Returns a numeric vector with names corresponding to the spectrum names.

scanIndex

scanIndex(signature(object="OnDiskMSnExp")): get the spectra scan indices within the respective file. The relevant information is extracted from the object's featureData slot. Returns a numeric vector of indices with names corresponding to the spectrum names.

smoothed,smoothed<-

smoothed(signature(object="OnDiskMSnExp", msLevel. = "numeric")): whether individual spectra are smoothed or unsmoothed. The relevant information is extracted from the object's featureData slot. Returns a logical vector with names corresponding to the spectrum names. Use smoothed(object) <- value to update the information, with value being a logical vector of length equal to the number of spectra in the experiment.

spectra

spectra(signature(object="OnDiskMSnExp"), BPPARAM=bpparam()): extract spectrum data from the individual files. This causes the spectrum data to be read from the original raw files. After that all processing steps defined in the spectraProcessingQueue are applied to it. The results are then returned as a list of Spectrum1 objects.

The BPPARAM argument can be used to define how and if parallel processing should be used. Information from individual files will be processed in parallel (one process per file). Note: extraction of selected spectra results in a considerable processing speed and should thus be preferred over whole data extraction.

Returns a list of Spectrum1 objects with names corresponding to the spectrum names.

tic

tic(signature(object="OnDiskMSnExp"), initial = TRUE, BPPARAM = bpparam()): get the total ion current (TIC) of each spectrum in the data set. If initial = TRUE, the information is extracted from the object's featureData and represents the tic provided in the header of the original raw data files. For initial = FALSE, the TIC is calculated from the actual intensity values in each spectrum after applying all data manipulation methods (if any).

See also https://github.com/lgatto/MSnbase/issues/332 for more details.

BPPARAM parameter: see spectra method above.

Returns a numeric vector with names corresponding to the spectrum names.

bpi

bpi(signature(object="OnDiskMSnExp"), initial = TRUE, BPPARAM = bpparam()): get the base peak intensity (BPI), i.e. the maximum intensity from each spectrum in the data set. If initial = TRUE, the information is extracted from the object's featureData and represents the bpi provided in the header of the original raw data files. For initial = FALSE, the BPI is calculated from the actual intensity values in each spectrum after applying all eventual data manipulation methods.

See also https://github.com/lgatto/MSnbase/issues/332 for more details.

BPPARAM parameter: see spectra method above.

Returns a numeric vector with names corresponding to the spectrum names.

featureNames

tic(signature(object="OnDiskMSnExp")): return a character of length length(object) containing the feature names. A replacement method is also available.

spectrapply

spectrapply(signature(object = "OnDiskMSnExp"), FUN = NULL, BPPARAM = bpparam(), ...): applies the function FUN to each spectrum passing additional parameters in ... to that function and return its results. For FUN = NULL it returns the list of spectra (same as a call to spectra). Parameter BPPARAM allows to specify how and if parallel processing should be enabled.

Returns a list with the result for each of spectrum.

Data manipulation methods

(in alphabetical order) See also methods for MSnExp or pSet objects. In contrast to the same-named methods for pSet or MSnExp classes, the actual data manipulation is not performed immediately, but only on-demand, e.g. when intensity or M/Z values are loaded.

clean

clean(signature(object="OnDiskMSnExp"), all=TRUE, verbose=TRUE): add an clean processing step to the lazy processing queue of the OnDiskMSnExp object. The clean command will only be executed when spectra information (including M/Z and intensity values) is requested from the OnDiskMSnExp object. Optional arguments to the methods are all=TRUE and verbose=TRUE.

The method returns an OnDiskMSnExp object.

For more details see documentation of the clean method.

normalize

normalize(signature(object="OnDiskMSnExp"), method=c("max", "sum"), ...): add a normalize processing step to the lazy processing queue of the returned OnDiskMSnExp object.

The method returns an OnDiskMSnExp object.

For more details see documentation of the normalize method.

removePeaks

removePeaks(signature(object="OnDiskMSnExp"), t="min", verbose=TRUE): add a removePeaks processing step to the lazy processing queue of the returned OnDiskMSnExp object.

The method returns an OnDiskMSnExp object.

For more details see documentation of the removePeaks method.

trimMz

trimMz(signature(object="OnDiskMSnExp", mzlim="numeric"),...): add a trimMz processing step to the lazy processing queue of the returned OnDiskMSnExp object.

The method returns an OnDiskMSnExp object.

For more details see documentation of the trimMz method.

Other methods and functions

validateOnDiskMSnExp: validateOnDiskMSnExp(signature(object = "OnDiskMSnExp")): validates an OnDiskMSnExp object and all of its spectra. In addition to the standard validObject method, this method reads also all spectra from the original files, applies eventual processing steps and evaluates their validity.
as(from, "MSnExp"): Converts the OnDiskMSnExp object from, to an in-memory MSnExp. Also available as an S3 method as.MSnExp().

Author

Johannes Rainer <johannes.rainer@eurac.edu>

Examples

mzfile <- MsDataHub::X20171016_POOL_POS_1_105.134.mzML()
#> see ?MsDataHub and browseVignettes('MsDataHub') for documentation
#> loading from cache

## Read the data as an OnDiskMSnExp
odmse <- readMSData(mzfile, msLevel. = 1, centroided. = TRUE)

## Get the length of data, i.e. the total number of spectra.
length(odmse)
#> [1] 931

## Get the MS level
head(msLevel(odmse))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>       1       1       1       1       1       1 

## Get the featureData, use fData to return as a data.frame
head(fData(odmse))
#>         spectrum
#> F1.S001        1
#> F1.S002        2
#> F1.S003        3
#> F1.S004        4
#> F1.S005        5
#> F1.S006        6

## Get to know from which file the spectra are
head(fromFile(odmse))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>       1       1       1       1       1       1 

## And the file names:
fileNames(odmse)
#> [1] "/github/home/.cache/R/ExperimentHub/61921ea20ba5_7859"

## Scan index and acquisitionNum
head(scanIndex(odmse))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>       1       2       3       4       5       6 
head(acquisitionNum(odmse))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>       1       2       3       4       5       6 

## Extract the spectra; the data is retrieved from the raw files.
head(spectra(odmse))
#> $F1.S001
#> Object of class "Spectrum1"
#>  Retention time: 0:00 
#>  MSn level: 1 
#>  Total ion count: 578 
#>  Polarity: 1 
#> 
#> $F1.S002
#> Object of class "Spectrum1"
#>  Retention time: 0:01 
#>  MSn level: 1 
#>  Total ion count: 1529 
#>  Polarity: 1 
#> 
#> $F1.S003
#> Object of class "Spectrum1"
#>  Retention time: 0:01 
#>  MSn level: 1 
#>  Total ion count: 1600 
#>  Polarity: 1 
#> 
#> $F1.S004
#> Object of class "Spectrum1"
#>  Retention time: 0:01 
#>  MSn level: 1 
#>  Total ion count: 1664 
#>  Polarity: 1 
#> 
#> $F1.S005
#> Object of class "Spectrum1"
#>  Retention time: 0:01 
#>  MSn level: 1 
#>  Total ion count: 1417 
#>  Polarity: 1 
#> 
#> $F1.S006
#> Object of class "Spectrum1"
#>  Retention time: 0:02 
#>  MSn level: 1 
#>  Total ion count: 1602 
#>  Polarity: 1 
#> 

## Extracting individual spectra or a subset is much faster.
spectra(odmse[1:50])
#> $F1.S001
#> Object of class "Spectrum1"
#>  Retention time: 0:00 
#>  MSn level: 1 
#>  Total ion count: 578 
#>  Polarity: 1 
#> 
#> $F1.S002
#> Object of class "Spectrum1"
#>  Retention time: 0:01 
#>  MSn level: 1 
#>  Total ion count: 1529 
#>  Polarity: 1 
#> 
#> $F1.S003
#> Object of class "Spectrum1"
#>  Retention time: 0:01 
#>  MSn level: 1 
#>  Total ion count: 1600 
#>  Polarity: 1 
#> 
#> $F1.S004
#> Object of class "Spectrum1"
#>  Retention time: 0:01 
#>  MSn level: 1 
#>  Total ion count: 1664 
#>  Polarity: 1 
#> 
#> $F1.S005
#> Object of class "Spectrum1"
#>  Retention time: 0:01 
#>  MSn level: 1 
#>  Total ion count: 1417 
#>  Polarity: 1 
#> 
#> $F1.S006
#> Object of class "Spectrum1"
#>  Retention time: 0:02 
#>  MSn level: 1 
#>  Total ion count: 1602 
#>  Polarity: 1 
#> 
#> $F1.S007
#> Object of class "Spectrum1"
#>  Retention time: 0:02 
#>  MSn level: 1 
#>  Total ion count: 1468 
#>  Polarity: 1 
#> 
#> $F1.S008
#> Object of class "Spectrum1"
#>  Retention time: 0:02 
#>  MSn level: 1 
#>  Total ion count: 1440 
#>  Polarity: 1 
#> 
#> $F1.S009
#> Object of class "Spectrum1"
#>  Retention time: 0:03 
#>  MSn level: 1 
#>  Total ion count: 1496 
#>  Polarity: 1 
#> 
#> $F1.S010
#> Object of class "Spectrum1"
#>  Retention time: 0:03 
#>  MSn level: 1 
#>  Total ion count: 1431 
#>  Polarity: 1 
#> 
#> $F1.S011
#> Object of class "Spectrum1"
#>  Retention time: 0:03 
#>  MSn level: 1 
#>  Total ion count: 1489 
#>  Polarity: 1 
#> 
#> $F1.S012
#> Object of class "Spectrum1"
#>  Retention time: 0:03 
#>  MSn level: 1 
#>  Total ion count: 1349 
#>  Polarity: 1 
#> 
#> $F1.S013
#> Object of class "Spectrum1"
#>  Retention time: 0:04 
#>  MSn level: 1 
#>  Total ion count: 1650 
#>  Polarity: 1 
#> 
#> $F1.S014
#> Object of class "Spectrum1"
#>  Retention time: 0:04 
#>  MSn level: 1 
#>  Total ion count: 1697 
#>  Polarity: 1 
#> 
#> $F1.S015
#> Object of class "Spectrum1"
#>  Retention time: 0:04 
#>  MSn level: 1 
#>  Total ion count: 1413 
#>  Polarity: 1 
#> 
#> $F1.S016
#> Object of class "Spectrum1"
#>  Retention time: 0:04 
#>  MSn level: 1 
#>  Total ion count: 1593 
#>  Polarity: 1 
#> 
#> $F1.S017
#> Object of class "Spectrum1"
#>  Retention time: 0:05 
#>  MSn level: 1 
#>  Total ion count: 1560 
#>  Polarity: 1 
#> 
#> $F1.S018
#> Object of class "Spectrum1"
#>  Retention time: 0:05 
#>  MSn level: 1 
#>  Total ion count: 1477 
#>  Polarity: 1 
#> 
#> $F1.S019
#> Object of class "Spectrum1"
#>  Retention time: 0:05 
#>  MSn level: 1 
#>  Total ion count: 1536 
#>  Polarity: 1 
#> 
#> $F1.S020
#> Object of class "Spectrum1"
#>  Retention time: 0:06 
#>  MSn level: 1 
#>  Total ion count: 1491 
#>  Polarity: 1 
#> 
#> $F1.S021
#> Object of class "Spectrum1"
#>  Retention time: 0:06 
#>  MSn level: 1 
#>  Total ion count: 1575 
#>  Polarity: 1 
#> 
#> $F1.S022
#> Object of class "Spectrum1"
#>  Retention time: 0:06 
#>  MSn level: 1 
#>  Total ion count: 1503 
#>  Polarity: 1 
#> 
#> $F1.S023
#> Object of class "Spectrum1"
#>  Retention time: 0:06 
#>  MSn level: 1 
#>  Total ion count: 1543 
#>  Polarity: 1 
#> 
#> $F1.S024
#> Object of class "Spectrum1"
#>  Retention time: 0:07 
#>  MSn level: 1 
#>  Total ion count: 1604 
#>  Polarity: 1 
#> 
#> $F1.S025
#> Object of class "Spectrum1"
#>  Retention time: 0:07 
#>  MSn level: 1 
#>  Total ion count: 1443 
#>  Polarity: 1 
#> 
#> $F1.S026
#> Object of class "Spectrum1"
#>  Retention time: 0:07 
#>  MSn level: 1 
#>  Total ion count: 1579 
#>  Polarity: 1 
#> 
#> $F1.S027
#> Object of class "Spectrum1"
#>  Retention time: 0:08 
#>  MSn level: 1 
#>  Total ion count: 1390 
#>  Polarity: 1 
#> 
#> $F1.S028
#> Object of class "Spectrum1"
#>  Retention time: 0:08 
#>  MSn level: 1 
#>  Total ion count: 1436 
#>  Polarity: 1 
#> 
#> $F1.S029
#> Object of class "Spectrum1"
#>  Retention time: 0:08 
#>  MSn level: 1 
#>  Total ion count: 1626 
#>  Polarity: 1 
#> 
#> $F1.S030
#> Object of class "Spectrum1"
#>  Retention time: 0:08 
#>  MSn level: 1 
#>  Total ion count: 1552 
#>  Polarity: 1 
#> 
#> $F1.S031
#> Object of class "Spectrum1"
#>  Retention time: 0:09 
#>  MSn level: 1 
#>  Total ion count: 1501 
#>  Polarity: 1 
#> 
#> $F1.S032
#> Object of class "Spectrum1"
#>  Retention time: 0:09 
#>  MSn level: 1 
#>  Total ion count: 1516 
#>  Polarity: 1 
#> 
#> $F1.S033
#> Object of class "Spectrum1"
#>  Retention time: 0:09 
#>  MSn level: 1 
#>  Total ion count: 1537 
#>  Polarity: 1 
#> 
#> $F1.S034
#> Object of class "Spectrum1"
#>  Retention time: 0:09 
#>  MSn level: 1 
#>  Total ion count: 1386 
#>  Polarity: 1 
#> 
#> $F1.S035
#> Object of class "Spectrum1"
#>  Retention time: 0:10 
#>  MSn level: 1 
#>  Total ion count: 1452 
#>  Polarity: 1 
#> 
#> $F1.S036
#> Object of class "Spectrum1"
#>  Retention time: 0:10 
#>  MSn level: 1 
#>  Total ion count: 1578 
#>  Polarity: 1 
#> 
#> $F1.S037
#> Object of class "Spectrum1"
#>  Retention time: 0:10 
#>  MSn level: 1 
#>  Total ion count: 1513 
#>  Polarity: 1 
#> 
#> $F1.S038
#> Object of class "Spectrum1"
#>  Retention time: 0:11 
#>  MSn level: 1 
#>  Total ion count: 1520 
#>  Polarity: 1 
#> 
#> $F1.S039
#> Object of class "Spectrum1"
#>  Retention time: 0:11 
#>  MSn level: 1 
#>  Total ion count: 1489 
#>  Polarity: 1 
#> 
#> $F1.S040
#> Object of class "Spectrum1"
#>  Retention time: 0:11 
#>  MSn level: 1 
#>  Total ion count: 1399 
#>  Polarity: 1 
#> 
#> $F1.S041
#> Object of class "Spectrum1"
#>  Retention time: 0:11 
#>  MSn level: 1 
#>  Total ion count: 1545 
#>  Polarity: 1 
#> 
#> $F1.S042
#> Object of class "Spectrum1"
#>  Retention time: 0:12 
#>  MSn level: 1 
#>  Total ion count: 1440 
#>  Polarity: 1 
#> 
#> $F1.S043
#> Object of class "Spectrum1"
#>  Retention time: 0:12 
#>  MSn level: 1 
#>  Total ion count: 1565 
#>  Polarity: 1 
#> 
#> $F1.S044
#> Object of class "Spectrum1"
#>  Retention time: 0:12 
#>  MSn level: 1 
#>  Total ion count: 1330 
#>  Polarity: 1 
#> 
#> $F1.S045
#> Object of class "Spectrum1"
#>  Retention time: 0:13 
#>  MSn level: 1 
#>  Total ion count: 1580 
#>  Polarity: 1 
#> 
#> $F1.S046
#> Object of class "Spectrum1"
#>  Retention time: 0:13 
#>  MSn level: 1 
#>  Total ion count: 1524 
#>  Polarity: 1 
#> 
#> $F1.S047
#> Object of class "Spectrum1"
#>  Retention time: 0:13 
#>  MSn level: 1 
#>  Total ion count: 1410 
#>  Polarity: 1 
#> 
#> $F1.S048
#> Object of class "Spectrum1"
#>  Retention time: 0:13 
#>  MSn level: 1 
#>  Total ion count: 1397 
#>  Polarity: 1 
#> 
#> $F1.S049
#> Object of class "Spectrum1"
#>  Retention time: 0:14 
#>  MSn level: 1 
#>  Total ion count: 1520 
#>  Polarity: 1 
#> 
#> $F1.S050
#> Object of class "Spectrum1"
#>  Retention time: 0:14 
#>  MSn level: 1 
#>  Total ion count: 1650 
#>  Polarity: 1 
#> 

## Alternatively, we could also subset the whole object by spectra and/or samples:
subs <- odmse[rtime(odmse) >= 2 & rtime(odmse) <= 20, ]
fileNames(subs)
#> [1] "/github/home/.cache/R/ExperimentHub/61921ea20ba5_7859"
rtime(subs)
#> F1.S008 F1.S009 F1.S010 F1.S011 F1.S012 F1.S013 F1.S014 F1.S015 F1.S016 F1.S017 
#>   2.233   2.512   2.791   3.070   3.349   3.628   3.907   4.186   4.465   4.744 
#> F1.S018 F1.S019 F1.S020 F1.S021 F1.S022 F1.S023 F1.S024 F1.S025 F1.S026 F1.S027 
#>   5.023   5.302   5.581   5.860   6.139   6.418   6.697   6.976   7.255   7.534 
#> F1.S028 F1.S029 F1.S030 F1.S031 F1.S032 F1.S033 F1.S034 F1.S035 F1.S036 F1.S037 
#>   7.813   8.092   8.371   8.650   8.929   9.208   9.487   9.766  10.045  10.324 
#> F1.S038 F1.S039 F1.S040 F1.S041 F1.S042 F1.S043 F1.S044 F1.S045 F1.S046 F1.S047 
#>  10.603  10.882  11.161  11.440  11.719  11.998  12.277  12.556  12.835  13.114 
#> F1.S048 F1.S049 F1.S050 F1.S051 F1.S052 F1.S053 F1.S054 F1.S055 F1.S056 F1.S057 
#>  13.393  13.672  13.951  14.230  14.509  14.788  15.067  15.346  15.625  15.904 
#> F1.S058 F1.S059 F1.S060 F1.S061 F1.S062 F1.S063 F1.S064 F1.S065 F1.S066 F1.S067 
#>  16.183  16.462  16.741  17.020  17.299  17.578  17.857  18.136  18.415  18.694 
#> F1.S068 F1.S069 F1.S070 F1.S071 
#>  18.973  19.252  19.531  19.810 

## Extract intensities and M/Z values per spectrum; the methods return a list,
## each element representing the values for one spectrum.
ints <- intensity(odmse)
mzs <- mz(odmse)

## Return a data.frame with mz and intensity pairs for each spectrum from the
## object
res <- spectrapply(odmse, FUN = as, Class = "data.frame")

## Calling removePeaks, i.e. setting intensity values below a certain threshold to 0.
## Unlike the name suggests, this is not actually removing peaks. Such peaks with a 0
## intensity are then removed by the "clean" step.
## Also, the manipulations are not applied directly, but put into the "lazy"
## processing queue.
odmse <- removePeaks(odmse, t=10000)
odmse <- clean(odmse)

## The processing steps are only applied when actual raw data is extracted.
spectra(odmse[1:2])
#> $F1.S001
#> Object of class "Spectrum1"
#>  Retention time: 0:00 
#>  MSn level: 1 
#>  Total ion count: 20 
#>  Polarity: 1 
#> 
#> $F1.S002
#> Object of class "Spectrum1"
#>  Retention time: 0:01 
#>  MSn level: 1 
#>  Total ion count: 21 
#>  Polarity: 1 
#> 

## Get the polarity of the spectra.
head(polarity(odmse))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>       1       1       1       1       1       1 

## Get the retention time of all spectra
head(rtime(odmse))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>   0.280   0.559   0.838   1.117   1.396   1.675 

## Get the intensities after removePeaks and clean
intsAfter <- intensity(odmse)

head(lengths(ints))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>     578    1529    1600    1664    1417    1602 
head(lengths(intsAfter))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>      20      21      21      23      22      24 

## The same for the M/Z values
mzsAfter <- intensity(odmse)
head(lengths(mzs))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>     578    1529    1600    1664    1417    1602 
head(lengths(mzsAfter))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>      20      21      21      23      22      24 

## Centroided or profile mode
f <- MsDataHub::MS3TMT11.mzML()
#> see ?MsDataHub and browseVignettes('MsDataHub') for documentation
#> loading from cache

odmse <- readMSData(f, mode = "onDisk")
validObject(odmse)
#> [1] TRUE
odmse[[1]]
#> Object of class "Spectrum1"
#>  Retention time: 45:27 
#>  MSn level: 1 
#>  Total ion count: 10768 
#>  Polarity: 1 

table(isCentroidedFromFile(odmse), msLevel(odmse))
#> < table of extent 0 x 3 >

## centroided status could be set manually
centroided(odmse, msLevel = 1) <- FALSE
centroided(odmse, msLevel = 2) <- TRUE
centroided(odmse, msLevel = 3) <- TRUE

## or when reading the data
odmse2 <- readMSData(f, centroided = c(FALSE, TRUE, TRUE),
                     mode = "onDisk")
table(centroided(odmse), msLevel(odmse))
#>        
#>           1   2   3
#>   FALSE  30   0   0
#>   TRUE    0 482 482

## Filtering precursor scans

head(acquisitionNum(odmse))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>   21945   21946   21947   21948   21949   21950 
head(msLevel(odmse))
#> F1.S001 F1.S002 F1.S003 F1.S004 F1.S005 F1.S006 
#>       1       2       2       3       2       2 

## Extract all spectra stemming from the first MS1 spectrum
(from1 <- filterPrecursorScan(odmse, 21945))
#> MSn experiment data ("OnDiskMSnExp")
#> Object size in memory: 0.05 Mb
#> - - - Spectra data - - -
#>  MS level(s): 1 2 3 
#>  Number of spectra: 35 
#>  MSn retention times: 45:27 - 45:30 minutes
#> - - - Processing information - - -
#> Data loaded [Thu Oct 29 09:04:07 2026] 
#> Filter: select parent/children scans for 21945 [Thu Oct 29 09:04:08 2026] 
#>  MSnbase version: 2.39.6 
#> - - - Meta data  - - -
#> phenoData
#>   rowNames: 61925a2e4f2a_10476
#>   varLabels: sampleNames
#>   varMetadata: labelDescription
#> Loaded from:
#>   61925a2e4f2a_10476 
#> protocolData: none
#> featureData
#>   featureNames: F1.S001 F1.S002 ... F1.S035 (35 total)
#>   fvarLabels: fileIdx spIdx ... spectrum (36 total)
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
table(msLevel(from1))
#> 
#>  1  2  3 
#>  1 17 17 


## Extract the second sepctrum's parent (MS1) and children (MS3)
## spectra
(from2 <- filterPrecursorScan(odmse, 21946))
#> MSn experiment data ("OnDiskMSnExp")
#> Object size in memory: 0.03 Mb
#> - - - Spectra data - - -
#>  MS level(s): 1 2 3 
#>  Number of spectra: 3 
#>  MSn retention times: 45:27 - 45:27 minutes
#> - - - Processing information - - -
#> Data loaded [Thu Oct 29 09:04:07 2026] 
#> Filter: select parent/children scans for 21946 [Thu Oct 29 09:04:08 2026] 
#>  MSnbase version: 2.39.6 
#> - - - Meta data  - - -
#> phenoData
#>   rowNames: 61925a2e4f2a_10476
#>   varLabels: sampleNames
#>   varMetadata: labelDescription
#> Loaded from:
#>   61925a2e4f2a_10476 
#> protocolData: none
#> featureData
#>   featureNames: F1.S001 F1.S002 F1.S004
#>   fvarLabels: fileIdx spIdx ... spectrum (36 total)
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
table(msLevel(from2))
#> 
#> 1 2 3 
#> 1 1 1